LMU BioDB 2024 - User contributions [en]

Nstojan1 Week 5

2024-02-14T16:58:26Z

Nstojan1: Added sections

==Purpose==
==Questions==
==Acknowledgments==
==References==

Template:Nstojan1

2024-02-08T23:01:21Z

Nstojan1: /* Individual Journal Entry */ edited syntax

== Assignment Page ==
[[Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Nstojan1 Week 5]]

[[Week 6]]

== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

Template:Nstojan1

2024-02-08T23:00:19Z

Nstojan1: /* Shared Journal Entry */ edited syntax

== Assignment Page ==
[[Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Week 5]]

[[Week 6]]

== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

AgeAnnoMO Week 4

2024-02-08T08:09:31Z

Nstojan1: added presentation

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

== General information about the database ==

=== What is the name of the database? (link to the home page)===
AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

=== What type (or types) of database is it?===

AgeAnnoMO is a Multi Omics Database for animal aging.

=== What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) ===
It contains age-related genes, proteins, metabolites, mitochondrial genes, microbiota and age-specific TCR and BCR sequences relating to aging for 50 different species.

=== What type of data source does it have? ===

Secondary data from other databases such as PubMed and Google Scholar.

=== Primary versus secondary ("meta")? ===

AgeAnnoMO is a secondary (meta) source since they collected the data from previous studies.

=== curated versus non-curated? ===
Curated

=== if curated, is it electronic versus human curation? ===
AgeAnnoMO seems to be created through human curation because the species and the datasets are handpicked.

=== if human curation, is it in-house staff versus community curation? ===

This databases is curated by in house staff, not community curation.

=== What individual or organization maintains the database? ===

UT Health, West China School of Medicine, and Xidian University are mentioned in this database, however it is unclear if individuals or organizations actually maintain it.

=== Public versus private? ===
AgeAnnoMO is a database available to the public.

=== Large national or multinational entity or small lab group ===

This appears to be a multinational entity with contributors being UT health, West China School of Medicine, Xidian University. However, after examining this database, it seems that a small lab group most likely put this database together.

=== What is their funding source(s)? ===

Funding has been provided through each of the three universities involved in creating this database.

== Scientific quality of the database: ==

=== Does the content appear to completely cover its content domain? ===

The content of this database does not completely cover its content domain.

=== *How many records does the database contain? ===

136 aging datasets.

=== What claims do the database owners make about coverage in the corresponding paper? ===

Welcome to AgeAnnoMO!

Aging is a complex process characterized by the progressive decline in various biological systems at molecular, cellular, tissue, and organ levels. To understand the underlying mechanisms, twelve hallmarks have been identified as common factors contributing to aging. These hallmarks are demonstrated to be remarkable conservation across multiple species. Understanding the regulation of aging factors and their relationships across species can facilitate the translation of anti -aging drug development from model organisms to humans.

Here, we built AgeAnnoMO, a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8,586 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, aging-related proteins, metabolites, mitochondrial genes, microbiotas, and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology, and identifying the targetable biomarkers for aging research.

=== *What species are covered in the database? (If it is a very long list, summarize.) ===

The database claims to cover 50 species, but when browsing the variety of species there is only 20 available including humans, rabbits, mice, and fish.

=== *Is the database content useful? I.e., what biological questions can it be used to answer? ===

The database content is useful because it contains two ways a user may browse through the information. A variety of hallmarks that contribute to aging is available, and a user may click on the different functions that contribute to aging, such as genomic instability, mitochondrial dysfunction, dysbiosis in aging, etc. If there is a particular species of interest, the content within this database is neatly organized into 50 various species, in which users can click on the species to browse information on their animal of interest.

=== Is the database content timely? ===

Yes, the database content is timely, as it is updated yearly.

=== Is there a need in the scientific community for such a database at this time? ===
No.

=== Is the content covered by other databases already? ===
The content is covered by other larger databases that provide more information in a simplified way.

=== How current is the database? ===
The datasets depending on species range back from 2015-2022.

=== When did the database first go online? ===

The database first went online in 2015.

=== How often is the database updated? ===

This database is updated yearly, with publications spanning from 2015 to 2023. There has been nothing new in 2024 published.

=== When was the last update? ===

2023.

=== General utility of the database to the scientific community ===
I do not see this database as being a utility to the scientific community unless a person wanted to know about a specific aging factor. They could easily access the Gene ID and search it on a larger database. Even then, I think directly going to the database would be easier because there are no hyperlinks or direct access to the information.

=== Are there links to other databases? Which ones? ===
There are links to similar databases. GenAge, AgingAtlas, The Digital Aging Atlas, AnAge, AGEMAP, Open Genes

Related Projects:
GenAge
GenAge: a genomic and proteomic network map of human ageing.

AgingAtlas
Aging Atlas: a multi-omics database for aging biology.

The Digital Ageing Atlas
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

AnAge
A database of vertebrate longevity records and their relation to other life history traits.

AGEMAP
AGEMAP: A Gene Expression Database for Aging in Mice.

=== Is it convenient to browse the data? ===

Browsing data is convenient because it is very user friendly and easy to navigate. However, once you click on the datasets for the specific species or aging contributors, the way the data is displayed is a little unclear, as it is presented in tiny rows with words half cut off, as well as including blurry pictures of graphs and tables.

=== Is it convenient to download the data? ===
The data is not convenient to download, it comes in the form of excel files with numerous columns and rows and does not simplify the information presented in any way. It just seems like a raw file.

=== In what file formats are the data provided? ===

.xlsx

=== What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? ===

From the database:

All results files can be downloaded in Github or Zenodo:
github link
zenodo link

The file extension .xlsx is used.

=== Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? ===

Files that can be downloaded in Github or Zenodo are non-standard formats.

The file extension .xlsx is used, which is standard format.

Raw data is also used which is non-standard.

=== Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? ===
The database is not that user friendly. While you can access specific type of information such as different age contributing factors and specific species. The information presented is inconsistent and does not simplify the information found. The information is presented in a confusing way, nothing is hyperlinked and to gather more information the databases they got their datasets from must be used.

=== Is the website well-organized? ===

The website is well-organized on the exterior. Users are able to browse by species or browse by hallmarks of aging. Engaging graphics are utilized to capture user attention. However, when clicking on the subject of interest, the data is unclear. For many of the species, after clicking on one, very little information is given with no context. The only data shown is the number, species, tissue, project ID, and sequencing technique, such as mass spectroscopy. No other information is given, such as what the sequencing technique was used for, etc. This leaves users confused and with little information to analyze.

=== Does it have a help section or tutorial? ===

Yes, this database has a help section but not a tutorial section. However, the help section is not very useful, as it seems to have just inserted pictures from different aspects of the site instead of telling users how to navigate and interpret each dataset.

=== Are the search options sensible? ===
The search option is sensible, you can select the data type and they will list the species available that have data. Unless you know the exact Gene ID/Entry ID, there will still be a lot of data shown if the species is common such as mice.

=== Run a sample query. Do the results make sense? ===
The results do not make sense. It is hard to see what the point of the information is, there are some typos and you can't click on anything. There are graphs present but it does not allow you to zoom in or click on it to expand the picture so you can't see what its clearly showing unless you go to the database they got the information from and look at those findings. They don't provide information about the numbers or the ways the experiment was from and how they got results. The headings are unclear and there are not legends or keys that explain what graphs are showing.

=== Access: Is there a license agreement or any restrictions on access to the database? ===

Yes, copyright 2023-Present.

== Summary judgment: ==
=== Would you direct a colleague unfamiliar with the field to use it? ===

No, I would not direct a colleague unfamiliar with the field to use the AgeAnnoMO database because of its lack of information and lack of details on the data it claims to provide.

=== Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur. ===

This database seems to be a hobby, contributed to by three universities across the world. This database is limited in scope and does seem amateur.

==Presentation==

[[File:The_AgeAnnoMo_Database.pdf]]

== References: ==

AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

== Acknowledgements: ==

Natalija and I (Charlotte) met Tuesday January 6th to work on our assignment. We met again Wednesday January 7th to create our powerpoint. We also communicated over text.
All work is ours unless noted otherwise.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 16:16, 7 February 2024 (PST)

File:The AgeAnnoMo Database.pdf

2024-02-08T08:08:37Z

Nstojan1: Presentation

== Summary ==
Presentation

Class Journal Week 4

2024-02-08T08:06:36Z

Nstojan1: /* Natalija */ answered question

Class Journal Week 4

==Andrew Sandler==

To User Page: [[User: Asandle1]]

To Assignment Page: [[Week 4]]

[[Category:Shared]]
[[Category:Journal Entry]]
<hr>

<b>1). Name two core competencies I am most skilled with or most familiar with from the list. Where and how did I gain the skills/become familiar?</b>

I am good with data conversion and interoperability and data preservation. I learned the skills of data conversion through my use of a mac and pc and having to transfer different programs and files between the two, where it isn't as simple as just emailing the file. For example .exe works on macs, but .bat doesn't. Yet it works fine on windows. I have less experience with Linux. I gained the skills of data preservation through my own research over the last few years trying to figure out the best way to protect my photos from over the years in a format that would work in the future and in a place they would be safe.

<b>2). The core competencies I want to know more about.</b>

I want to know more about the discovery of data, specifically on knowing what data is actually relevant and what is not. I also want to learn more about Data Management and Organization since I don't know how it works at all.

====Andrew Sandler's References====

=====Acknowledgements=====

- Used the first week's template with Dean to base this week's journal on.

- All work is my own except where acknowledged otherwise. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 16:59, 7 February 2024 (PST)

===== Bibliography =====

* [[Week 4| Assignment Page]]

* [https://xmlpipedb.cs.lmu.edu/biodb/spring2024/images/8/8b/L02_DataSharing.pptx DataOne powerpoint pt 2]

[[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 13:47, 7 February 2024 (PST)

==Charlotte==

[[User: Ckapla12]]

[[Week 4]]

*Name two of these core competencies are you most skilled with (or which is most familiar to you)? Where and how did you gain the skills/become familiar?
The two core competencies I am most familiar with are data preservation and data analysis. In regards to data preservation, I am familiar with saving and organizing data properly through tools such as excel. I have had to do this for many lab courses, so I've learned about it through training and practice. For data analysis, I am familiar with looking at data and finding patterns. I've learned this through school work, such as labs and math courses, which allowed me to work with different types of data.

*Name two of these core competencies that you want to know more about? Why?
Data curation and re-use is something I want to learn how to manage data well from start to finish. Knowing about data curation will teach me how to organize, maintain, and save data properly. Also, it will help me understand how to make data usable again, which is important for better data management. I know little to nothing about data curation and reuse. Data analysis is also something I would like to know more about. By learning different analysis methods, I can find important information in complex data.

=== References: ===

[[Week 4| Assignment Page]]

[https://xmlpipedb.cs.lmu.edu/biodb/spring2024/images/8/8b/L02_DataSharing.pptx DataOne powerpoint pt 2]

=== Acknowledgments ===
The work completed above has been done by me. [[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 20:50, 7 February 2024 (PST)

==Hailey==
'''Name two of these core competencies are you most skilled with (or which is most familiar to you)? Where and how did you gain the skills/become familiar?'''
# Data Visualization. In class, with the graph of the day puzzles, we get to practice our data visualization skills. While I've never correctly guessed one of the graphs, I feel like my thought process is good for deducing what a graph could be or is comprised of and why.
# Discovery and Acquisition of Data. Throughout my academic career at LMU, while not database-focused, I think I have learned how to find appropriate sources of information. I have learned about how to find academic papers specifically and what makes a good source versus a bad source for academic writing, and I think these skills are similar to and can be extended to discovery and acquisition of data.
'''Name two of these core competencies that you want to know more about? Why?'''
# Ethics, including citation of data. While I know that I can't plagiarize or copy-paste images without citation, I don't have a complete grasp on different licensing, as I'm not used to publishing things publicly on the internet. I would like to learn more about this such that I can avoid copyright infringement and use information fairly and effectively.
# Databases and Data Formats. I do not know what a relational database is, nor am I certain whether I'm familiar or not with common data types that would be involved in a relational database. Because I am clueless to most components of this competency, I think it would serve me well to comb through and learn more about it.

==Katie==
1. I would say I am most familiar with Discovery and Acquisition of Data, and Ethics, including citation of data. I have developed the skills required to discover and acquire data throughout my academic career. I would argue that this started when I first learned what an encyclopedia was and knew that in order to locate specific data, I would have to choose the corresponding book based on its letter. My AP Biology class was probably my first experience with locating data repositories in the scientific field and ensuring that it was a reputable and trustworthy source. My classes at LMU have helped me to further develop this skill. I would also I am familiar with the ethics surrounding data. This is another skill that I learned at a young age, which is the importance of your own intellectual property and not using another person’s. If you do use something that doesn’t belong to you, you must cite it. This applies to data repositories and citation of data. If you are going to take data from another source, you must cite it. This week has helped me learn more about proper accreditation for taking from another database and how it is important for both for those who run the database and those who use it.

2. I want to know more about Data Analysis and Data Visualization. I feel that these are two skills that go together well and both are needed to understand each other. I think these are both really important skills for not just those who work with data, but any person in their daily life. Knowing how to analyze data and how its visualized ensures that a person cannot be influenced by improper or biased representations of data.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:04, 7 February 2024 (PST)

==Dean==
#Two competencies that I am most skilled with are Databases and data formats, and ethics, including citation of data. I have become familiar with querying databases and becoming familiar with data types and formats through years of using databases for school and for projects. I have used biological databases since high school for assignments and have since learned several techniques on how to navigate them and how to find the type and format of data that I am looking for. I am also familiar with the ethics and data citation competency because through my training as a psychology major, I have learned several rules about how to ethically acquire and utilize data, especially that which is from human subjects.
#The two competencies that I am least familiar with are metadata and data preservation. I am unfamiliar with metadata because I do not know how to interpret metadata from eternal sources at this point. I have little experience working with metadata or annotating data so it can be used by other users. Not much of the work I have done has incorporated metadata strictly speaking. I also am not familiar with methods of preserving data over long periods of time since I know that certain standards and techniques for data change over time.

==Natalija==
#I think I'm most familiar with the ethics of data because of my education in the United States. Prior to attending school here, I never understood the importance of citing data. In Europe, especially in highschools this isn’t emphasized at all. When I moved to the United States, I struggled a lot with learning how to properly use information and give credit where it is due. Even though I believe I have gotten better with it, I know that I still struggle with it to this day just because there is so many ways to cite data. Through my classes, especially at LMU, I’ve learned a lot about how to properly use, share and access data which at times involved getting permission and licenses. Another skill I am familiar with is visualizing data. I think that taking STEM classes at LMU has given me the ability to understand data that is given in the form of visuals. Even during this class, I’ve seen how my confidence has developed in interpreting different kinds of graphs and charts presented.

#I would love to learn more about data analysis, I’ve seen how efficient it can be especially with large datasets. When I was working on this project, I got to explore GitHub which I found very interesting especially because it seems to be such a collaborative platform. I think that another thing I would like to learn more about is data conversion and interoperability. I never really understood the importance of formats and why we use some formats compared to others.

AgeAnnoMO Week 4

2024-02-07T00:30:06Z

Nstojan1: /* What individual or organization maintains the database? */ edit answer

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

== General information about the database ==

=== What is the name of the database? (link to the home page)===
AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

=== What type (or types) of database is it?===

AgeAnnoMO is a Multi Omics Database for animal aging.

=== What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) ===
It contains age-related genes, proteins, metabolites, mitochondrial genes, microbiota and age-specific TCR and BCR sequences relating to aging for 50 different species.

=== What type of data source does it have? ===

Secondary data from other databases such as PubMed and Google Scholar.

=== Primary versus secondary ("meta")? ===

AgeAnnoMO is a secondary (meta) source since they collected the data from previous studies.

=== curated versus non-curated? ===
Curated

=== if curated, is it electronic versus human curation? ===
AgeAnnoMO seems to be created through human curation because the species and the datasets are handpicked.

=== if human curation, is it in-house staff versus community curation? ===

This databases is curated by in house staff, not community curation.

=== What individual or organization maintains the database? ===

UT Health, West China School of Medicine, and Xidian University are mentioned in this database, however it is unclear if individuals or organizations actually maintain it.

=== Public versus private? ===
AgeAnnoMO is a database available to the public.

=== Large national or multinational entity or small lab group ===
This is a multinational entity with contributors being UT health, West China School of Medicine, Xidian University.

=== What is their funding source(s)? ===

Funding has been provided through each of the three universities involved in creating this database.

== Scientific quality of the database: ==

=== Does the content appear to completely cover its content domain? ===

The content of this database does not completely cover its content domain.

=== *How many records does the database contain? ===

136 aging datasets.

=== What claims do the database owners make about coverage in the corresponding paper? ===

Welcome to AgeAnnoMO!

Aging is a complex process characterized by the progressive decline in various biological systems at molecular, cellular, tissue, and organ levels. To understand the underlying mechanisms, twelve hallmarks have been identified as common factors contributing to aging. These hallmarks are demonstrated to be remarkable conservation across multiple species. Understanding the regulation of aging factors and their relationships across species can facilitate the translation of anti -aging drug development from model organisms to humans.

Here, we built AgeAnnoMO, a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8,586 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, aging-related proteins, metabolites, mitochondrial genes, microbiotas, and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology, and identifying the targetable biomarkers for aging research.

=== *What species are covered in the database? (If it is a very long list, summarize.) ===

The database claims to cover 50 species, but when browsing the variety of species there is only 20 available including humans, rabbits, mice, and fish.

=== *Is the database content useful? I.e., what biological questions can it be used to answer? ===

The database content is useful because it contains two ways a user may browse through the information. A variety of hallmarks that contribute to aging is available, and a user may click on the different functions that contribute to aging, such as genomic instability, mitochondrial dysfunction, dysbiosis in aging, etc. If there is a particular species of interest, the content within this database is neatly organized into 50 various species, in which users can click on the species to browse information on their animal of interest.

=== Is the database content timely? ===

Yes, the database content is timely, as it is updated yearly.

=== Is there a need in the scientific community for such a database at this time? ===
No.

=== Is the content covered by other databases already? ===
The content is covered by other larger databases that provide more information in a simplified way.

=== How current is the database? ===
The datasets depending on species range back from 2015-2022.

=== When did the database first go online? ===

The database first went online in 2018.

=== How often is the database updated? ===

This database is updated yearly, with publications spanning from 2018 to current time 2024.

=== When was the last update? ===

2023.

=== General utility of the database to the scientific community ===
I do not see this database as being a utility to the scientific community unless a person wanted to know about a specific aging factor. They could easily access the Gene ID and search it on a larger database. Even then, I think directly going to the database would be easier because there are no hyperlinks or direct access to the information.

=== Are there links to other databases? Which ones? ===
There are links to similar databases. GenAge, AgingAtlas, The Digital Aging Atlas, AnAge, AGEMAP, Open Genes

Related Projects:
GenAge
GenAge: a genomic and proteomic network map of human ageing.

AgingAtlas
Aging Atlas: a multi-omics database for aging biology.

The Digital Ageing Atlas
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

AnAge
A database of vertebrate longevity records and their relation to other life history traits.

AGEMAP
AGEMAP: A Gene Expression Database for Aging in Mice.

=== Is it convenient to browse the data? ===

Browsing data is convenient because it is very user friendly and easy to navigate. However, once you click on the datasets for the specific species or aging contributors, the way the data is displayed is a little unclear, as it is presented in tiny rows with words half cut off, as well as including blurry pictures of graphs and tables.

=== Is it convenient to download the data? ===
The data is not convenient to download, it comes in the form of excel files with numerous columns and rows and does not simplify the information presented in any way. It just seems like a raw file.

=== In what file formats are the data provided? ===

.xlsx

=== What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? ===

From the database:

All results files can be downloaded in Github or Zenodo:
github link
zenodo link

The file extension .xlsx is used.

=== Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? ===

Files that can be downloaded in Github or Zenodo are non-standard formats.

The file extension .xlsx is used, which is standard format.

Raw data is also used which is non-standard.

=== Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? ===
The database is not that user friendly. While you can access specific type of information such as different age contributing factors and specific species. The information presented is inconsistent and does not simplify the information found. The information is presented in a confusing way, nothing is hyperlinked and to gather more information the databases they got their datasets from must be used.

=== Is the website well-organized? ===

The website is well-organized on the exterior. Users are able to browse by species or browse by hallmarks of aging. Engaging graphics are utilized to capture user attention. However, when clicking on the subject of interest, the data is unclear. For many of the species, after clicking on one, very little information is given with no context. The only data shown is the number, species, tissue, project ID, and sequencing technique, such as mass spectroscopy. No other information is given, such as what the sequencing technique was used for, etc. This leaves users confused and with little information to analyze.

=== Does it have a help section or tutorial? ===

Yes, this database has a help section but not a tutorial section. However, the help section is not very useful, as it seems to have just inserted pictures from different aspects of the site instead of telling users how to navigate and interpret each dataset.

=== Are the search options sensible? ===
The search option is sensible, you can select the data type and they will list the species available that have data. Unless you know the exact Gene ID/Entry ID, there will still be a lot of data shown if the species is common such as mice.

=== Run a sample query. Do the results make sense? ===
The results do not make sense. It is hard to see what the point of the information is, there are some typos and you can't click on anything. There are graphs present but it does not allow you to zoom in or click on it to expand the picture so you can't see what its clearly showing unless you go to the database they got the information from and look at those findings. They don't provide information about the numbers or the ways the experiment was from and how they got results. The headings are unclear and there are not legends or keys that explain what graphs are showing.

=== Access: Is there a license agreement or any restrictions on access to the database? ===

Yes, copyright 2023-Present.

== Summary judgment: ==
=== Would you direct a colleague unfamiliar with the field to use it? ===

No, I would not direct a colleague unfamiliar with the field to use the AgeAnnoMO database because of its lack of information and lack of details on the data it claims to provide.

=== Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur. ===

This database seems to be a hobby, contributed to by three universities across the world. This database is limited in scope and does seem amateur.

AgeAnnoMO Week 4

2024-02-07T00:26:06Z

Nstojan1: /* Run a sample query. Do the results make sense? */ answered question

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

== General information about the database ==

=== What is the name of the database? (link to the home page)===
AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

=== What type (or types) of database is it?===

AgeAnnoMO is a Multi Omics Database for animal aging.

=== What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) ===
It contains age-related genes, proteins, metabolites, mitochondrial genes, microbiota and age-specific TCR and BCR sequences relating to aging for 50 different species.

=== What type of data source does it have? ===

Secondary data from other databases such as PubMed and Google Scholar.

=== Primary versus secondary ("meta")? ===

AgeAnnoMO is a secondary (meta) source since they collected the data from previous studies.

=== curated versus non-curated? ===
Curated

=== if curated, is it electronic versus human curation? ===
AgeAnnoMO seems to be created through human curation because the species and the datasets are handpicked.

=== if human curation, is it in-house staff versus community curation? ===

This databases is curated by in house staff, not community curation.

=== What individual or organization maintains the database? ===

UT Health, West China School of Medicine, and Xidian University maintains this database.

=== Public versus private? ===
AgeAnnoMO is a database available to the public.

=== Large national or multinational entity or small lab group ===
This is a multinational entity with contributors being UT health, West China School of Medicine, Xidian University.

=== What is their funding source(s)? ===

Funding has been provided through each of the three universities involved in creating this database.

== Scientific quality of the database: ==

=== Does the content appear to completely cover its content domain? ===

The content of this database does not completely cover its content domain.

=== *How many records does the database contain? ===

136 aging datasets.

=== What claims do the database owners make about coverage in the corresponding paper? ===

Welcome to AgeAnnoMO!

Aging is a complex process characterized by the progressive decline in various biological systems at molecular, cellular, tissue, and organ levels. To understand the underlying mechanisms, twelve hallmarks have been identified as common factors contributing to aging. These hallmarks are demonstrated to be remarkable conservation across multiple species. Understanding the regulation of aging factors and their relationships across species can facilitate the translation of anti -aging drug development from model organisms to humans.

Here, we built AgeAnnoMO, a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8,586 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, aging-related proteins, metabolites, mitochondrial genes, microbiotas, and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology, and identifying the targetable biomarkers for aging research.

=== *What species are covered in the database? (If it is a very long list, summarize.) ===

The database claims to cover 50 species, but when browsing the variety of species there is only 20 available including humans, rabbits, mice, and fish.

=== *Is the database content useful? I.e., what biological questions can it be used to answer? ===

The database content is useful because it contains two ways a user may browse through the information. A variety of hallmarks that contribute to aging is available, and a user may click on the different functions that contribute to aging, such as genomic instability, mitochondrial dysfunction, dysbiosis in aging, etc. If there is a particular species of interest, the content within this database is neatly organized into 50 various species, in which users can click on the species to browse information on their animal of interest.

=== Is the database content timely? ===

Yes, the database content is timely, as it is updated yearly.

=== Is there a need in the scientific community for such a database at this time? ===
No.

=== Is the content covered by other databases already? ===
The content is covered by other larger databases that provide more information in a simplified way.

=== How current is the database? ===
The datasets depending on species range back from 2015-2022.

=== When did the database first go online? ===

The database first went online in 2018.

=== How often is the database updated? ===

This database is updated yearly, with publications spanning from 2018 to current time 2024.

=== When was the last update? ===

2023.

=== General utility of the database to the scientific community ===
I do not see this database as being a utility to the scientific community unless a person wanted to know about a specific aging factor. They could easily access the Gene ID and search it on a larger database. Even then, I think directly going to the database would be easier because there are no hyperlinks or direct access to the information.

=== Are there links to other databases? Which ones? ===
There are links to similar databases. GenAge, AgingAtlas, The Digital Aging Atlas, AnAge, AGEMAP, Open Genes

Related Projects:
GenAge
GenAge: a genomic and proteomic network map of human ageing.

AgingAtlas
Aging Atlas: a multi-omics database for aging biology.

The Digital Ageing Atlas
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

AnAge
A database of vertebrate longevity records and their relation to other life history traits.

AGEMAP
AGEMAP: A Gene Expression Database for Aging in Mice.

=== Is it convenient to browse the data? ===

Browsing data is convenient because it is very user friendly and easy to navigate. However, once you click on the datasets for the specific species or aging contributors, the way the data is displayed is a little unclear, as it is presented in tiny rows with words half cut off, as well as including blurry pictures of graphs and tables.

=== Is it convenient to download the data? ===
The data is not convenient to download, it comes in the form of excel files with numerous columns and rows and does not simplify the information presented in any way. It just seems like a raw file.

=== In what file formats are the data provided? ===

.xlsx

=== What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? ===

From the database:

All results files can be downloaded in Github or Zenodo:
github link
zenodo link

The file extension .xlsx is used.

=== Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? ===

=== Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? ===
The database is not that user friendly. While you can access specific type of information such as different age contributing factors and specific species. The information presented is inconsistent and does not simplify the information found. The information is presented in a confusing way, nothing is hyperlinked and to gather more information the databases they got their datasets from must be used.

=== Is the website well-organized? ===

The website is well-organized on the exterior. Users are able to browse by species or browse by hallmarks of aging. Engaging graphics are utilized to capture user attention. However, when clicking on the subject of interest, the data is unclear. For many of the species, after clicking on one, very little information is given with no context. The only data shown is the number, species, tissue, project ID, and sequencing technique, such as mass spectroscopy. No other information is given, such as what the sequencing technique was used for, etc. This leaves users confused and with little information to analyze.

=== Does it have a help section or tutorial? ===

Yes, this database has a help section but not a tutorial section. However, the help section is not very useful, as it seems to have just inserted pictures from different aspects of the site instead of telling users how to navigate and interpret each dataset.

=== Are the search options sensible? ===
The search option is sensible, you can select the data type and they will list the species available that have data. Unless you know the exact Gene ID/Entry ID, there will still be a lot of data shown if the species is common such as mice.

=== Run a sample query. Do the results make sense? ===
The results do not make sense. It is hard to see what the point of the information is, there are some typos and you can't click on anything. There are graphs present but it does not allow you to zoom in or click on it to expand the picture so you can't see what its clearly showing unless you go to the database they got the information from and look at those findings. They don't provide information about the numbers or the ways the experiment was from and how they got results. The headings are unclear and there are not legends or keys that explain what graphs are showing.

=== Access: Is there a license agreement or any restrictions on access to the database? ===

Yes, copyright 2023-Present.

== Summary judgment: ==
=== Would you direct a colleague unfamiliar with the field to use it? ===

No, I would not direct a colleague unfamiliar with the field to use the AgeAnnoMO database because of its lack of information and lack of details on the data it claims to provide.

=== Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur. ===

This database seems to be a hobby, contributed to by three universities across the world. This database is limited in scope and does seem amateur.

AgeAnnoMO Week 4

2024-02-07T00:22:17Z

Nstojan1: /* Are the search options sensible? */ answered question

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

== General information about the database ==

=== What is the name of the database? (link to the home page)===
AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

=== What type (or types) of database is it?===

AgeAnnoMO is a Multi Omics Database for animal aging.

=== What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) ===
It contains age-related genes, proteins, metabolites, mitochondrial genes, microbiota and age-specific TCR and BCR sequences relating to aging for 50 different species.

=== What type of data source does it have? ===

Secondary data from other databases such as PubMed and Google Scholar.

=== Primary versus secondary ("meta")? ===

AgeAnnoMO is a secondary (meta) source since they collected the data from previous studies.

=== curated versus non-curated? ===
Curated

=== if curated, is it electronic versus human curation? ===
AgeAnnoMO seems to be created through human curation because the species and the datasets are handpicked.

=== if human curation, is it in-house staff versus community curation? ===

This databases is curated by in house staff, not community curation.

=== What individual or organization maintains the database? ===

UT Health, West China School of Medicine, and Xidian University maintains this database.

=== Public versus private? ===
AgeAnnoMO is a database available to the public.

=== Large national or multinational entity or small lab group ===
This is a multinational entity with contributors being UT health, West China School of Medicine, Xidian University.

=== What is their funding source(s)? ===

Funding has been provided through each of the three universities involved in creating this database.

== Scientific quality of the database: ==

=== Does the content appear to completely cover its content domain? ===

The content of this database does not completely cover its content domain.

=== *How many records does the database contain? ===

136 aging datasets.

=== What claims do the database owners make about coverage in the corresponding paper? ===

Welcome to AgeAnnoMO!

Aging is a complex process characterized by the progressive decline in various biological systems at molecular, cellular, tissue, and organ levels. To understand the underlying mechanisms, twelve hallmarks have been identified as common factors contributing to aging. These hallmarks are demonstrated to be remarkable conservation across multiple species. Understanding the regulation of aging factors and their relationships across species can facilitate the translation of anti -aging drug development from model organisms to humans.

Here, we built AgeAnnoMO, a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8,586 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, aging-related proteins, metabolites, mitochondrial genes, microbiotas, and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology, and identifying the targetable biomarkers for aging research.

=== *What species are covered in the database? (If it is a very long list, summarize.) ===

The database claims to cover 50 species, but when browsing the variety of species there is only 20 available including humans, rabbits, mice, and fish.

=== *Is the database content useful? I.e., what biological questions can it be used to answer? ===

The database content is useful because it contains two ways a user may browse through the information. A variety of hallmarks that contribute to aging is available, and a user may click on the different functions that contribute to aging, such as genomic instability, mitochondrial dysfunction, dysbiosis in aging, etc. If there is a particular species of interest, the content within this database is neatly organized into 50 various species, in which users can click on the species to browse information on their animal of interest.

=== Is the database content timely? ===

Yes, the database content is timely, as it is updated yearly.

=== Is there a need in the scientific community for such a database at this time? ===
No.

=== Is the content covered by other databases already? ===
The content is covered by other larger databases that provide more information in a simplified way.

=== How current is the database? ===
The datasets depending on species range back from 2015-2022.

=== When did the database first go online? ===

The database first went online in 2018.

=== How often is the database updated? ===

This database is updated yearly, with publications spanning from 2018 to current time 2024.

=== When was the last update? ===

=== General utility of the database to the scientific community ===
I do not see this database as being a utility to the scientific community unless a person wanted to know about a specific aging factor. They could easily access the Gene ID and search it on a larger database. Even then, I think directly going to the database would be easier because there are no hyperlinks or direct access to the information.

=== Are there links to other databases? Which ones? ===
There are links to similar databases. GenAge, AgingAtlas, The Digital Aging Atlas, AnAge, AGEMAP, Open Genes

Related Projects:
GenAge
GenAge: a genomic and proteomic network map of human ageing.

AgingAtlas
Aging Atlas: a multi-omics database for aging biology.

The Digital Ageing Atlas
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

AnAge
A database of vertebrate longevity records and their relation to other life history traits.

AGEMAP
AGEMAP: A Gene Expression Database for Aging in Mice.

=== Is it convenient to browse the data? ===

Browsing data is convenient because it is very user friendly and easy to navigate. However, once you click on the datasets for the specific species or aging contributors, the way the data is displayed is a little unclear, as it is presented in tiny rows with words half cut off, as well as including blurry pictures of graphs and tables.

=== Is it convenient to download the data? ===
The data is not convenient to download, it comes in the form of excel files with numerous columns and rows and does not simplify the information presented in any way. It just seems like a raw file.

=== In what file formats are the data provided? ===

.xlsx

=== What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? ===

From the database:

All results files can be downloaded in Github or Zenodo:
github link
zenodo link

The file extension .xlsx is used.

=== Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? ===

=== Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? ===
The database is not that user friendly. While you can access specific type of information such as different age contributing factors and specific species. The information presented is inconsistent and does not simplify the information found. The information is presented in a confusing way, nothing is hyperlinked and to gather more information the databases they got their datasets from must be used.

=== Is the website well-organized? ===

The website is well-organized on the exterior. Users are able to browse by species or browse by hallmarks of aging. Engaging graphics are utilized to capture user attention. However, when clicking on the subject of interest, the data is unclear. For many of the species, after clicking on one, very little information is given with no context. The only data shown is the number, species, tissue, project ID, and sequencing technique, such as mass spectroscopy. No other information is given, such as what the sequencing technique was used for, etc. This leaves users confused and with little information to analyze.

=== Does it have a help section or tutorial? ===

Yes, this database has a help section but not a tutorial section. However, the help section is not very useful, as it seems to have just inserted pictures from different aspects of the site instead of telling users how to navigate and interpret each dataset.

=== Are the search options sensible? ===
The search option is sensible, you can select the data type and they will list the species available that have data. Unless you know the exact Gene ID/Entry ID, there will still be a lot of data shown if the species is common such as mice.

=== Run a sample query. Do the results make sense? ===

=== Access: Is there a license agreement or any restrictions on access to the database? ===

== Summary judgment: ==
=== Would you direct a colleague unfamiliar with the field to use it? ===

Yes, I would direct a colleague unfamiliar with the field to use the AgeAnnoMO database because of its multifaceted design and easy to navigate layout.

=== Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur. ===

This is a professional database contributed to by three universities across the world. This database is not limited in scope and does not seem amateur.

AgeAnnoMO Week 4

2024-02-07T00:19:31Z

Nstojan1: /* Is there a need in the scientific community for such a database at this time? */ answered question

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

== General information about the database ==

=== What is the name of the database? (link to the home page)===
AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

=== What type (or types) of database is it?===

AgeAnnoMO is a Multi Omics Database for animal aging.

=== What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) ===
It contains age-related genes, proteins, metabolites, mitochondrial genes, microbiota and age-specific TCR and BCR sequences relating to aging for 50 different species.

=== What type of data source does it have? ===

Secondary data from other databases such as PubMed and Google Scholar.

=== Primary versus secondary ("meta")? ===

AgeAnnoMO is a secondary (meta) source since they collected the data from previous studies.

=== curated versus non-curated? ===
Curated

=== if curated, is it electronic versus human curation? ===
AgeAnnoMO seems to be created through human curation because the species and the datasets are handpicked.

=== if human curation, is it in-house staff versus community curation? ===

This databases is curated by in house staff, not community curation.

=== What individual or organization maintains the database? ===

UT Health, West China School of Medicine, and Xidian University maintains this database.

=== Public versus private? ===
AgeAnnoMO is a database available to the public.

=== Large national or multinational entity or small lab group ===
This is a multinational entity with contributors being UT health, West China School of Medicine, Xidian University.

=== What is their funding source(s)? ===

Funding has been provided through each of the three universities involved in creating this database.

== Scientific quality of the database: ==

=== Does the content appear to completely cover its content domain? ===

The content of this database does not completely cover its content domain.

=== *How many records does the database contain? ===

136 aging datasets.

=== What claims do the database owners make about coverage in the corresponding paper? ===

=== *What species are covered in the database? (If it is a very long list, summarize.) ===

The database claims to cover 50 species, but when browsing the variety of species there is only 20 available including humans, rabbits, mice, and fish.

=== *Is the database content useful? I.e., what biological questions can it be used to answer? ===

The database content is useful because it contains two ways a user may browse through the information. A variety of hallmarks that contribute to aging is available, and a user may click on the different functions that contribute to aging, such as genomic instability, mitochondrial dysfunction, dysbiosis in aging, etc. If there is a particular species of interest, the content within this database is neatly organized into 50 various species, in which users can click on the species to browse information on their animal of interest.

=== Is the database content timely? ===

Yes, the database content is timely, as it is updated yearly.

=== Is there a need in the scientific community for such a database at this time? ===
No.

=== Is the content covered by other databases already? ===
The content is covered by other larger databases that provide more information in a simplified way.

=== How current is the database? ===
The datasets depending on species range back from 2015-2022.

=== When did the database first go online? ===

The database first went online in 2018.

=== How often is the database updated? ===

This database is updated yearly, with publications spanning from 2018 to current time 2024.

=== When was the last update? ===

=== General utility of the database to the scientific community ===
I do not see this database as being a utility to the scientific community unless a person wanted to know about a specific aging factor. They could easily access the Gene ID and search it on a larger database. Even then, I think directly going to the database would be easier because there are no hyperlinks or direct access to the information.

=== Are there links to other databases? Which ones? ===
There are links to similar databases. GenAge, AgingAtlas, The Digital Aging Atlas, AnAge, AGEMAP, Open Genes

Related Projects:
GenAge
GenAge: a genomic and proteomic network map of human ageing.

AgingAtlas
Aging Atlas: a multi-omics database for aging biology.

The Digital Ageing Atlas
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

AnAge
A database of vertebrate longevity records and their relation to other life history traits.

AGEMAP
AGEMAP: A Gene Expression Database for Aging in Mice.

=== Is it convenient to browse the data? ===

Browsing data is convenient because it is very user friendly and easy to navigate. However, once you click on the datasets for the specific species or aging contributors, the way the data is displayed is a little unclear, as it is presented in tiny rows with words half cut off, as well as including blurry pictures of graphs and tables.

=== Is it convenient to download the data? ===
The data is not convenient to download, it comes in the form of excel files with numerous columns and rows and does not simplify the information presented in any way. It just seems like a raw file.

=== In what file formats are the data provided? ===

.xlsx

=== What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? ===

From the database:

All results files can be downloaded in Github or Zenodo:
github link
zenodo link

The file extension .xlsx is used.

=== Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? ===

=== Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? ===
The database is not that user friendly. While you can access specific type of information such as different age contributing factors and specific species. The information presented is inconsistent and does not simplify the information found. The information is presented in a confusing way, nothing is hyperlinked and to gather more information the databases they got their datasets from must be used.

=== Is the website well-organized? ===

The website is well-organized on the exterior. Users are able to browse by species or browse by hallmarks of aging. Engaging graphics are utilized to capture user attention. However, when clicking on the subject of interest, the data is unclear. For many of the species, after clicking on one, very little information is given with no context. The only data shown is the number, species, tissue, project ID, and sequencing technique, such as mass spectroscopy. No other information is given, such as what the sequencing technique was used for, etc. This leaves users confused and with little information to analyze.

=== Does it have a help section or tutorial? ===

Yes, this database has a help section but not a tutorial section. However, the help section is not very useful, as it seems to have just inserted pictures from different aspects of the site instead of telling users how to navigate and interpret each dataset.

=== Are the search options sensible? ===

=== Run a sample query. Do the results make sense? ===

=== Access: Is there a license agreement or any restrictions on access to the database? ===

== Summary judgment: ==
=== Would you direct a colleague unfamiliar with the field to use it? ===

Yes, I would direct a colleague unfamiliar with the field to use the AgeAnnoMO database because of its multifaceted design and easy to navigate layout.

=== Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur. ===

This is a professional database contributed to by three universities across the world. This database is not limited in scope and does not seem amateur.

AgeAnnoMO Week 4

2024-02-07T00:19:12Z

Nstojan1: /* General utility of the database to the scientific community */ answered question

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

== General information about the database ==

=== What is the name of the database? (link to the home page)===
AgeAnnoMO https://relab.xidian.edu.cn/AgeAnnoMO/#/

=== What type (or types) of database is it?===

AgeAnnoMO is a Multi Omics Database for animal aging.

=== What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) ===
It contains age-related genes, proteins, metabolites, mitochondrial genes, microbiota and age-specific TCR and BCR sequences relating to aging for 50 different species.

=== What type of data source does it have? ===

Secondary data from other databases such as PubMed and Google Scholar.

=== Primary versus secondary ("meta")? ===

AgeAnnoMO is a secondary (meta) source since they collected the data from previous studies.

=== curated versus non-curated? ===
Curated

=== if curated, is it electronic versus human curation? ===
AgeAnnoMO seems to be created through human curation because the species and the datasets are handpicked.

=== if human curation, is it in-house staff versus community curation? ===

This databases is curated by in house staff, not community curation.

=== What individual or organization maintains the database? ===

UT Health, West China School of Medicine, and Xidian University maintains this database.

=== Public versus private? ===
AgeAnnoMO is a database available to the public.

=== Large national or multinational entity or small lab group ===
This is a multinational entity with contributors being UT health, West China School of Medicine, Xidian University.

=== What is their funding source(s)? ===

Funding has been provided through each of the three universities involved in creating this database.

== Scientific quality of the database: ==

=== Does the content appear to completely cover its content domain? ===

The content of this database does not completely cover its content domain.

=== *How many records does the database contain? ===

136 aging datasets.

=== What claims do the database owners make about coverage in the corresponding paper? ===

=== *What species are covered in the database? (If it is a very long list, summarize.) ===

The database claims to cover 50 species, but when browsing the variety of species there is only 20 available including humans, rabbits, mice, and fish.

=== *Is the database content useful? I.e., what biological questions can it be used to answer? ===

The database content is useful because it contains two ways a user may browse through the information. A variety of hallmarks that contribute to aging is available, and a user may click on the different functions that contribute to aging, such as genomic instability, mitochondrial dysfunction, dysbiosis in aging, etc. If there is a particular species of interest, the content within this database is neatly organized into 50 various species, in which users can click on the species to browse information on their animal of interest.

=== Is the database content timely? ===

Yes, the database content is timely, as it is updated yearly.

=== Is there a need in the scientific community for such a database at this time? ===

=== Is the content covered by other databases already? ===
The content is covered by other larger databases that provide more information in a simplified way.

=== How current is the database? ===
The datasets depending on species range back from 2015-2022.

=== When did the database first go online? ===

The database first went online in 2018.

=== How often is the database updated? ===

This database is updated yearly, with publications spanning from 2018 to current time 2024.

=== When was the last update? ===

=== General utility of the database to the scientific community ===
I do not see this database as being a utility to the scientific community unless a person wanted to know about a specific aging factor. They could easily access the Gene ID and search it on a larger database. Even then, I think directly going to the database would be easier because there are no hyperlinks or direct access to the information.

=== Are there links to other databases? Which ones? ===
There are links to similar databases. GenAge, AgingAtlas, The Digital Aging Atlas, AnAge, AGEMAP, Open Genes

Related Projects:
GenAge
GenAge: a genomic and proteomic network map of human ageing.

AgingAtlas
Aging Atlas: a multi-omics database for aging biology.

The Digital Ageing Atlas
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

AnAge
A database of vertebrate longevity records and their relation to other life history traits.

AGEMAP
AGEMAP: A Gene Expression Database for Aging in Mice.

=== Is it convenient to browse the data? ===

Browsing data is convenient because it is very user friendly and easy to navigate. However, once you click on the datasets for the specific species or aging contributors, the way the data is displayed is a little unclear, as it is presented in tiny rows with words half cut off, as well as including blurry pictures of graphs and tables.

=== Is it convenient to download the data? ===
The data is not convenient to download, it comes in the form of excel files with numerous columns and rows and does not simplify the information presented in any way. It just seems like a raw file.

=== In what file formats are the data provided? ===

.xlsx

=== What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? ===

From the database:

All results files can be downloaded in Github or Zenodo:
github link
zenodo link

The file extension .xlsx is used.

=== Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? ===

=== Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? ===
The database is not that user friendly. While you can access specific type of information such as different age contributing factors and specific species. The information presented is inconsistent and does not simplify the information found. The information is presented in a confusing way, nothing is hyperlinked and to gather more information the databases they got their datasets from must be used.

=== Is the website well-organized? ===

The website is well-organized on the exterior. Users are able to browse by species or browse by hallmarks of aging. Engaging graphics are utilized to capture user attention. However, when clicking on the subject of interest, the data is unclear. For many of the species, after clicking on one, very little information is given with no context. The only data shown is the number, species, tissue, project ID, and sequencing technique, such as mass spectroscopy. No other information is given, such as what the sequencing technique was used for, etc. This leaves users confused and with little information to analyze.

=== Does it have a help section or tutorial? ===

Yes, this database has a help section but not a tutorial section. However, the help section is not very useful, as it seems to have just inserted pictures from different aspects of the site instead of telling users how to navigate and interpret each dataset.

=== Are the search options sensible? ===

=== Run a sample query. Do the results make sense? ===

=== Access: Is there a license agreement or any restrictions on access to the database? ===

== Summary judgment: ==
=== Would you direct a colleague unfamiliar with the field to use it? ===

Yes, I would direct a colleague unfamiliar with the field to use the AgeAnnoMO database because of its multifaceted design and easy to navigate layout.

=== Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur. ===

This is a professional database contributed to by three universities across the world. This database is not limited in scope and does not seem amateur.

AgeAnnoMO Week 4

2024-02-07T00:16:23Z

Nstojan1: /* Is the content covered by other databases already? */ answered question

AgeAnnoMO Week 4

2024-02-07T00:15:17Z

Nstojan1: /* Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? */ answered question

AgeAnnoMO Week 4

2024-02-07T00:11:28Z

Nstojan1: /* Is it convenient to download the data? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:35:43Z

Nstojan1: /* Is it convenient to browse the data? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:32:15Z

Nstojan1: /* Are there links to other databases? Which ones? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:27:17Z

Nstojan1: /* How current is the database? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:25:16Z

Nstojan1: /* Is the database content useful? I.e., what biological questions can it be used to answer? */ answer questions

AgeAnnoMO Week 4

2024-02-06T23:17:55Z

Nstojan1: /* What species are covered in the database? (If it is a very long list, summarize.) */ answered question

AgeAnnoMO Week 4

2024-02-06T23:15:44Z

Nstojan1: /* How many records does the database contain? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:13:13Z

Nstojan1: /* large national or multinational entity or small lab group */ answered question

AgeAnnoMO Week 4

2024-02-06T23:10:26Z

Nstojan1: /* if curated, is it electronic versus human curation? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:08:43Z

Nstojan1: /* curated versus non-curated? */ answered question

AgeAnnoMO Week 4

2024-02-06T23:04:05Z

Nstojan1: /* primary versus secondary ("meta")? */ answered questions

AgeAnnoMO Week 4

2024-02-06T23:03:24Z

Nstojan1: /* What type of data source does it have? */ answered question

AgeAnnoMO Week 4

2024-02-06T22:57:36Z

Nstojan1: /* What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?]) */ answered question

AgeAnnoMO Week 4

2024-02-06T22:52:47Z

Nstojan1: /* General information about the database */ answered question

Template:Nstojan1

2024-02-06T22:51:45Z

Nstojan1: /* Individual Journal Entry */ changed name of week 4

== Assignment Page ==
[[Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Week 5]]

[[Week 6]]

== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Journal Entry Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

ADHDgene Week 4

2024-02-06T22:41:34Z

Nstojan1: changed title

==AgeAnnoMo==

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

ADHDgene Week 4

2024-02-06T22:40:50Z

Nstojan1: /* hello */ added link

the shared wiki page for adhd gene week 4!!

[[https://relab.xidian.edu.cn/AgeAnnoMO/#/]]

Hivanson and Nstojan1 Week 3

2024-02-01T16:01:46Z

Nstojan1: /* Acknowledgments */ added acknowledgement

==IMD3==
===Summary of IMD3:===
''S. cerevisiae'' IMD3 is an Inosine-5′-monophosphate dehydrogenase (IMPDH) gene that is responsible for the catalysis of the rate-limiting step in ''de novo'' GTP synthesis. IMD3 is found in the cytoplasm of yeast cells and can bind metal ions, NAD, potassium, mRNA, and proteins. The function of IMD3’s mRNA binding capability is not known. The human orthologue of this gene is implicated in retinitis pigmentosa, a disease that causes blindness.

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**[https://www.yeastgenome.org/locus/S000004424 SGD ID:] S000004424
**[https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database ID:] 851152
**[https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl ID:]P50095 (referenced UniProt ID)
**[https://www.uniprot.org/uniprotkb/P50095/entry UniProt ID:] P50095
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate (IMP) to xanthosine 5’-phosphate (XMP) during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl and NCBI didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt and SGD have a lot of information that could be useful for a person studying IMD3 and its functions.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary. Notably, SGD had a fun visual for comparative information and UniProt had an equally fun visual to show the subcellular location of IMD3. While all sites were navigable, some were more user-friendly than others; UniProt was outstanding in this with an attractive and intuitive UI while Ensembl was lacking.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]

===Acknowledgments===
[[User:Nstojan1|Natalija]] and [[User:Hivanson|Hailey]] worked together on the IMD3 “My Favorite Gene” journal entry. We split up the work evenly based on what we felt most comfortable answering and helped each other throughout our working on the page at the end of class on 1/30/24 and via text on 1/31/24.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 22:16, 31 January 2024 (PST)

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Nstojan1|Nstojan1]] ([[User talk:Nstojan1|talk]]) 08:01, 1 February 2024 (PST)

===References===
*Database, A. P. S. (n.d.). Alphafold protein structure database. Retrieved January 31, 2024, from https://alphafold.ebi.ac.uk/entry/A0A816ADP2
*Firstglance in Jmol. (n.d.). Retrieved January 31, 2024, from https://proteopedia.org/wiki/fgij/
*Ford, P. (2015, June 11). What Is Code? Bloomberg. https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/
*Gene: IMD3 (YLR432W)—Summary—Saccharomyces_cerevisiae—Ensembl genome browser 111. (n.d.). Retrieved January 31, 2024, from https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA
*Help:Introduction to editing with Wiki Markup/2. (2021). In Wikipedia. Retrieved January 31, 2024, from https://en.wikipedia.org/w/index.php?title=Help:Introduction_to_editing_with_Wiki_Markup/2&oldid=1053961419
*IMD3—Inosine-5’-monophosphate dehydrogenase 3—Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker’s yeast) | UniProtKB | UniProt. (n.d.). Retrieved January 31, 2024, from https://www.uniprot.org/uniprotkb/P50095/entry
*IMD3. IMD3 | SGD. (n.d.). Retrieved January 31, 2024, from https://www.yeastgenome.org/locus/S000004424
*LMU BioDB 2024. (2024). Week 3. Retrieved January 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_3
*U.S. National Library of Medicine. (n.d.). IMD3 imp dehydrogenase imd3 [saccharomyces cerevisiae S288C] - gene - NCBI. National Center for Biotechnology Information. Retrieved January 31, 2024, from https://www.ncbi.nlm.nih.gov/gene/851152

Hivanson and Nstojan1 Week 3

2024-02-01T06:01:57Z

Nstojan1: /* References */ added citation

==IMD3==
===Summary of IMD3:===
''S. cerevisiae'' IMD3 is an Inosine-5′-monophosphate dehydrogenase (IMPDH) gene that is responsible for the catalysis of the rate-limiting step in ''de novo'' GTP synthesis. IMD3 is found in the cytoplasm of yeast cells and can bind metal ions, NAD, potassium, mRNA, and proteins. The function of IMD3’s mRNA binding capability is not known. The human orthologue of this gene is implicated in retinitis pigmentosa, a disease that causes blindness.

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**UniProtKB ID: P50095 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl and NCBI didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt and SGD have a lot of information that could be useful for a person studying IMD3 and its functions.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary. Notably, SGD had a fun visual for comparative information and UniProt had an equally fun visual to show the subcellular location of IMD3. While all sites were navigable, some were more user-friendly than others; UniProt was outstanding in this with an attractive and intuitive UI while Ensembl was lacking.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]
===Acknowledgments===
*Database, A. P. S. (n.d.). Alphafold protein structure database. https://alphafold.ebi.ac.uk/entry/A0A816ADP2
*Firstglance in Jmol. (n.d.). https://proteopedia.org/wiki/fgij/

===References===
*U.S. National Library of Medicine. (n.d.). IMD3 imp dehydrogenase imd3 [saccharomyces cerevisiae S288C] - gene - NCBI. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/gene/851152
*IMD3. IMD3 | SGD. (n.d.). https://www.yeastgenome.org/locus/S000004424

Hivanson and Nstojan1 Week 3

2024-02-01T06:00:41Z

Nstojan1: /* References */ added reference

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**UniProtKB ID: P50095 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl and NCBI didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt and SGD have a lot of information that could be useful for a person studying IMD3 and its functions.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary. Notably, SGD had a fun visual for comparative information and UniProt had an equally fun visual to show the subcellular location of IMD3. While all sites were navigable, some were more user-friendly than others; UniProt was outstanding in this with an attractive and intuitive UI while Ensembl was lacking.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]
===Acknowledgments===
*Database, A. P. S. (n.d.). Alphafold protein structure database. https://alphafold.ebi.ac.uk/entry/A0A816ADP2
*Firstglance in Jmol. (n.d.). https://proteopedia.org/wiki/fgij/

===References===
*U.S. National Library of Medicine. (n.d.). IMD3 imp dehydrogenase imd3 [saccharomyces cerevisiae S288C] - gene - NCBI. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/gene/851152

Hivanson and Nstojan1 Week 3

2024-02-01T05:57:11Z

Nstojan1: /* Acknowledgments */ added bullet and acknowledgement

Hivanson and Nstojan1 Week 3

2024-02-01T05:55:02Z

Nstojan1: /* Acknowledgments */ added acknowledgments

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**UniProtKB ID: P50095 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl and NCBI didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt and SGD have a lot of information that could be useful for a person studying IMD3 and its functions.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary. Notably, SGD had a fun visual for comparative information and UniProt had an equally fun visual to show the subcellular location of IMD3. While all sites were navigable, some were more user-friendly than others; UniProt was outstanding in this with an attractive and intuitive UI while Ensembl was lacking.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]
===Acknowledgments===
Database, A. P. S. (n.d.). Alphafold protein structure database. https://alphafold.ebi.ac.uk/entry/A0A816ADP2

===References===

Hivanson and Nstojan1 Week 3

2024-02-01T05:49:18Z

Nstojan1: edited syntax

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**UniProtKB ID: P50095 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt has a lot of information that could be useful for a person studying the gene.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]
===Acknowledgments===
===References===

Hivanson and Nstojan1 Week 3

2024-02-01T05:48:52Z

Nstojan1: added acknowledgments and references

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**UniProtKB ID: P50095 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate during the de novo synthesis of GTP. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt has a lot of information that could be useful for a person studying the gene.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]
==Acknowledgments==
==References==

User:Nstojan1

2024-02-01T05:45:56Z

Nstojan1: /* Acknowledgements */ edited syntax

== Natalija Stojanovic ==
=== Contact Information ===

Student
Loyola Marymount University
[http://www.lmu.edu LMU home page]
1 LMU, Drive MS 8888
Los Angeles, CA 90045
Email: nstojan1 at lion dot lmu dot edu

=== Education ===
* Biology, B.A., Loyola Marymount University, December 2024
* Upper division courses taken: Principles in Ecology, Biological Databases, Avian Biology Lab

=== Work Experience ===

# Working Student, MCP European Stables, Los Angeles, California, 2022-present
#* Training sales horse
#* Caring for horses
#* Barn chores
#* Helping during lessons
# Trail Guide, Los Angeles Horse Back Riding, Los Angeles, California, 2021-2022
#* Taking customers on trail rides
#* Taking care of customers
#* Filing paperwork
#* Taking care of horses

=== Personal Interests and Hobbies ===

* [[Media:Horse_.pdf|Horse Riding]]
* Photography
* Gym
* Cooking
* Travelling

[[Image:Greece.JPG|500px]]

==== Favorite Aspect of Biology ====

My favorite aspect about Biology is how complex and connected all of life is. Everything depends on each other and it's interesting to see the way different organisms interact with each other and the environment to sustain life.

==== Favorite Aspect of Computer Science ====

My favorite aspect of computer science is how you are able to apply it to a variety of fields. I have already seen personal potential and personal growth in just creating what you are reading!

===Career Goals===

In the future, I would definitely want to stay involved with horses and photography. I would love to own my own business training horses and traveling around the country to photograph the bigger competitions.

[[Template:Nstojan1]]
{{Template:Nstojan1}}

=== Acknowledgements ===

*I worked with [[User:Kmill104]]. We met outside of class and talked through text to help each other with the template problem.
* I met with [[User:Kdahlquist]] during office to get help with adding a picture and clarifying the template problem.
*Except for what is noted above, this individual journal entry was completed by me and not copied by another source.
*I worked with [[User:Hivanson]], we worked together in class and communicated via text to complete the assignment.

=== References ===

* LMU BioDB 2024. (2024). Week 1. Retrieved January 8, 2024, from https://xmlpipedb.cs.edu/biodb/Spring2024/index.php/Week_1
*Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

[[Category:Journal Entry]]

User:Nstojan1

2024-02-01T05:45:36Z

Nstojan1: /* Acknowledgements */ added acknowledgments

== Natalija Stojanovic ==
=== Contact Information ===

Student
Loyola Marymount University
[http://www.lmu.edu LMU home page]
1 LMU, Drive MS 8888
Los Angeles, CA 90045
Email: nstojan1 at lion dot lmu dot edu

=== Education ===
* Biology, B.A., Loyola Marymount University, December 2024
* Upper division courses taken: Principles in Ecology, Biological Databases, Avian Biology Lab

=== Work Experience ===

# Working Student, MCP European Stables, Los Angeles, California, 2022-present
#* Training sales horse
#* Caring for horses
#* Barn chores
#* Helping during lessons
# Trail Guide, Los Angeles Horse Back Riding, Los Angeles, California, 2021-2022
#* Taking customers on trail rides
#* Taking care of customers
#* Filing paperwork
#* Taking care of horses

=== Personal Interests and Hobbies ===

* [[Media:Horse_.pdf|Horse Riding]]
* Photography
* Gym
* Cooking
* Travelling

[[Image:Greece.JPG|500px]]

==== Favorite Aspect of Biology ====

My favorite aspect about Biology is how complex and connected all of life is. Everything depends on each other and it's interesting to see the way different organisms interact with each other and the environment to sustain life.

==== Favorite Aspect of Computer Science ====

My favorite aspect of computer science is how you are able to apply it to a variety of fields. I have already seen personal potential and personal growth in just creating what you are reading!

===Career Goals===

In the future, I would definitely want to stay involved with horses and photography. I would love to own my own business training horses and traveling around the country to photograph the bigger competitions.

[[Template:Nstojan1]]
{{Template:Nstojan1}}

=== Acknowledgements ===

*I worked with [[User:Kmill104]]. We met outside of class and talked through text to help each other with the template problem.
* I met with [[User:Kdahlquist]] during office to get help with adding a picture and clarifying the template problem.
*Except for what is noted above, this individual journal entry was completed by me and not copied by another source.
*I worked with [[Hivanson]], we worked together in class and communicated via text to complete the assignment.

=== References ===

* LMU BioDB 2024. (2024). Week 1. Retrieved January 8, 2024, from https://xmlpipedb.cs.edu/biodb/Spring2024/index.php/Week_1
*Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

[[Category:Journal Entry]]

Hivanson and Nstojan1 Week 3

2024-02-01T05:32:54Z

Nstojan1: added gene id

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**UniProtKB ID: P50095 [https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate, and during the de novo synthesis of GTP, it catalyzes the rate-limiting step. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**There were some differences in content; Ensembl didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt has a lot of information that could be useful for a person studying the gene.
**Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]

Hivanson and Nstojan1 Week 3

2024-02-01T05:31:44Z

Nstojan1: added gene id

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**SGD ID:S000004424 [https://www.yeastgenome.org/locus/S000004424 SGD:]
**Gene ID: 851152 [https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**[https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**UniProtKB ID: P50095 [https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate, and during the de novo synthesis of GTP, it catalyzes the rate-limiting step. It is also known to play an important role in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
**SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. Ensembl contains generic information that just covers the basics such as a name, description, and type.
**Were there differences in content, the information or data itself?
***There were some differences in content; Ensembl didn’t provide much information on the gene that would help one learn about it. On the other hand, UniProt has a lot of information that could be useful for a person studying the gene.
**Were there differences in presentation of the information?
***Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]

Class Journal Week 3

2024-02-01T04:18:03Z

Nstojan1: /* Reflection Questions */ deleted one signature

== Katie Miller ==
==== Reflection Questions ====
#Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you.
#What is something from the first two sections that you need further explanation of or that you want to know more about?
#Also, out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)
==== References ====
Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 17:09, 31 January 2024 (PST)

== Natalija Stojanovic ==
===Reflection Questions===
#A quote that really stood out to me was “Samsung makes computers that look like TVs, and Tesla makes computers with wheels and engines. Some things that aren’t yet computers–dental floss, flashlights–will fall eventually”. This quote stood out to me because it reminded me how much we have developed as a society in both positive and negative ways. The quote talks about how there are very few’ things that aren’t yet computers’, I feel like we have replaced so much with technology and it is upsetting to see because we have started to overuse and misuse it. It has completely taken over our lives, wherever you turn around there is some sort of computer. However, it has also greatly benefited us, people are able to do things so much more quickly and efficiently. Our daily lives have never been easier because of the help of computers, what used to take days and hours could be done in a matter of minutes or seconds.
#I didn’t understand what the author meant when he said “If you can sell the software, if you can light up the screen, you’re selling infinitely reproducible nothing. The margins on nothing are great–until other people start selling even cheaper nothings or giving them away”. When I first read this, I thought that the author was talking about the prices of softwares and how there is always someone that can make the software for cheaper or for free. I’m particularly confused as to why he calls them ‘nothings’.
#I liked the UniProt database the most because it was the easiest to use. All of the information was there and the page setup was extremely easy to navigate which was beneficial for someone like me that firstly knows nothing about the gene and secondly never used a database like that. I liked the large subheadings and informative subheadings. They described complex things in easy ways that I could comprehend and use in my research of the gene. My least favorite was Ensemble. It was so hard to navigate and understand what I was looking at. I felt as if there was nothing useful and half of the time I didn’t even understand what information they were providing me. It wasn't as user friendly and I probably would not use it again.
[[User:Nstojan1|Nstojan1]] ([[User talk:Nstojan1|talk]]) 20:16, 31 January 2024 (PST)

Class Journal Week 3

2024-02-01T04:17:46Z

Nstojan1: edited signature

Class Journal Week 3

2024-02-01T04:16:51Z

Nstojan1: added signature

User:Nstojan1

2024-02-01T04:15:39Z

Nstojan1: /* References */ added reference

== Natalija Stojanovic ==
=== Contact Information ===

Student
Loyola Marymount University
[http://www.lmu.edu LMU home page]
1 LMU, Drive MS 8888
Los Angeles, CA 90045
Email: nstojan1 at lion dot lmu dot edu

=== Education ===
* Biology, B.A., Loyola Marymount University, December 2024
* Upper division courses taken: Principles in Ecology, Biological Databases, Avian Biology Lab

=== Work Experience ===

# Working Student, MCP European Stables, Los Angeles, California, 2022-present
#* Training sales horse
#* Caring for horses
#* Barn chores
#* Helping during lessons
# Trail Guide, Los Angeles Horse Back Riding, Los Angeles, California, 2021-2022
#* Taking customers on trail rides
#* Taking care of customers
#* Filing paperwork
#* Taking care of horses

=== Personal Interests and Hobbies ===

* [[Media:Horse_.pdf|Horse Riding]]
* Photography
* Gym
* Cooking
* Travelling

[[Image:Greece.JPG|500px]]

==== Favorite Aspect of Biology ====

My favorite aspect about Biology is how complex and connected all of life is. Everything depends on each other and it's interesting to see the way different organisms interact with each other and the environment to sustain life.

==== Favorite Aspect of Computer Science ====

My favorite aspect of computer science is how you are able to apply it to a variety of fields. I have already seen personal potential and personal growth in just creating what you are reading!

===Career Goals===

In the future, I would definitely want to stay involved with horses and photography. I would love to own my own business training horses and traveling around the country to photograph the bigger competitions.

[[Template:Nstojan1]]
{{Template:Nstojan1}}

=== Acknowledgements ===

*I worked with [[User:Kmill104]]. We met outside of class and talked through text to help each other with the template problem.
* I met with [[User:Kdahlquist]] during office to get help with adding a picture and clarifying the template problem.
*Except for what is noted above, this individual journal entry was completed by me and not copied by another source.
*

=== References ===

* LMU BioDB 2024. (2024). Week 1. Retrieved January 8, 2024, from https://xmlpipedb.cs.edu/biodb/Spring2024/index.php/Week_1
*Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

[[Category:Journal Entry]]

Class Journal Week 3

2024-02-01T04:15:03Z

Nstojan1: Answered questions

== Katie Miller ==
==== Reflection Questions ====
#Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you.
#What is something from the first two sections that you need further explanation of or that you want to know more about?
#Also, out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)
==== References ====
Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 17:09, 31 January 2024 (PST)

== Natalija Stojanovic ==
#A quote that really stood out to me was “Samsung makes computers that look like TVs, and Tesla makes computers with wheels and engines. Some things that aren’t yet computers–dental floss, flashlights–will fall eventually”. This quote stood out to me because it reminded me how much we have developed as a society in both positive and negative ways. The quote talks about how there are very few’ things that aren’t yet computers’, I feel like we have replaced so much with technology and it is upsetting to see because we have started to overuse and misuse it. It has completely taken over our lives, wherever you turn around there is some sort of computer. However, it has also greatly benefited us, people are able to do things so much more quickly and efficiently. Our daily lives have never been easier because of the help of computers, what used to take days and hours could be done in a matter of minutes or seconds.
#I didn’t understand what the author meant when he said “If you can sell the software, if you can light up the screen, you’re selling infinitely reproducible nothing. The margins on nothing are great–until other people start selling even cheaper nothings or giving them away”. When I first read this, I thought that the author was talking about the prices of softwares and how there is always someone that can make the software for cheaper or for free. I’m particularly confused as to why he calls them ‘nothings’.
#I liked the UniProt database the most because it was the easiest to use. All of the information was there and the page setup was extremely easy to navigate which was beneficial for someone like me that firstly knows nothing about the gene and secondly never used a database like that. I liked the large subheadings and informative subheadings. They described complex things in easy ways that I could comprehend and use in my research of the gene. My least favorite was Ensemble. It was so hard to navigate and understand what I was looking at. I felt as if there was nothing useful and half of the time I didn’t even understand what information they were providing me. It wasn't as user friendly and I probably would not use it again.

User:Nstojan1

2024-02-01T03:43:20Z

Nstojan1: /* Acknowledgements */ added bullet point

== Natalija Stojanovic ==
=== Contact Information ===

Student
Loyola Marymount University
[http://www.lmu.edu LMU home page]
1 LMU, Drive MS 8888
Los Angeles, CA 90045
Email: nstojan1 at lion dot lmu dot edu

=== Education ===
* Biology, B.A., Loyola Marymount University, December 2024
* Upper division courses taken: Principles in Ecology, Biological Databases, Avian Biology Lab

=== Work Experience ===

# Working Student, MCP European Stables, Los Angeles, California, 2022-present
#* Training sales horse
#* Caring for horses
#* Barn chores
#* Helping during lessons
# Trail Guide, Los Angeles Horse Back Riding, Los Angeles, California, 2021-2022
#* Taking customers on trail rides
#* Taking care of customers
#* Filing paperwork
#* Taking care of horses

=== Personal Interests and Hobbies ===

* [[Media:Horse_.pdf|Horse Riding]]
* Photography
* Gym
* Cooking
* Travelling

[[Image:Greece.JPG|500px]]

==== Favorite Aspect of Biology ====

My favorite aspect about Biology is how complex and connected all of life is. Everything depends on each other and it's interesting to see the way different organisms interact with each other and the environment to sustain life.

==== Favorite Aspect of Computer Science ====

My favorite aspect of computer science is how you are able to apply it to a variety of fields. I have already seen personal potential and personal growth in just creating what you are reading!

===Career Goals===

In the future, I would definitely want to stay involved with horses and photography. I would love to own my own business training horses and traveling around the country to photograph the bigger competitions.

[[Template:Nstojan1]]
{{Template:Nstojan1}}

=== Acknowledgements ===

*I worked with [[User:Kmill104]]. We met outside of class and talked through text to help each other with the template problem.
* I met with [[User:Kdahlquist]] during office to get help with adding a picture and clarifying the template problem.
*Except for what is noted above, this individual journal entry was completed by me and not copied by another source.
*

=== References ===

* LMU BioDB 2024. (2024). Week 1. Retrieved January 8, 2024, from https://xmlpipedb.cs.edu/biodb/Spring2024/index.php/Week_1

[[Category:Journal Entry]]

Hivanson and Nstojan1 Week 3

2024-02-01T03:42:03Z

Nstojan1: edited answer

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**[https://www.yeastgenome.org/locus/S000004424 SGD:]
**[https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**[https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**[https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding.It catalyzes ionsine 5’-phosphate to xanthosine 5’-phosphate and during the de novo synthesis of GTP it catalyzes the rate limiting step. It is also known to play an important roll in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
***SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. e!Ensemble contains generic information that just covers the basics such as a name, description and type.
**Were there differences in content, the information or data itself?
***There were some differences in content, e!Ensemble didn’t really provide any information on the gene that would help one learn about it. On the other hand UniProt has a lot of information that could be useful for a person studying the gene.
**Were there differences in presentation of the information?
***Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]

Hivanson and Nstojan1 Week 3

2024-02-01T03:36:10Z

Nstojan1: /* IMD3 */ edited syntax

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**[https://www.yeastgenome.org/locus/S000004424 SGD:]
**[https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**[https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**[https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes the rate-limiting step in the de novo synthesis of GTP and its involved in GTP biosynthesis pathways. In addition, it catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP). It is also known to play an important roll in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
***SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. e!Ensemble contains generic information that just covers the basics such as a name, description and type.
**Were there differences in content, the information or data itself?
***There were some differences in content, e!Ensemble didn’t really provide any information on the gene that would help one learn about it. On the other hand UniProt has a lot of information that could be useful for a person studying the gene.
**Were there differences in presentation of the information?
***Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]

Hivanson and Nstojan1 Week 3

2024-02-01T03:35:21Z

Nstojan1: Added answers to questions

==IMD3==
===Summary of Function:===

===Other Information:===
*What is the standard name, systematic name, and name description for your gene (from SGD)?
**Standard name: IMD3
**Systematic name: YLR432W
**Name description: IMP Dehydrogenase
*What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
**[https://www.yeastgenome.org/locus/S000004424 SGD:]
**[https://www.ncbi.nlm.nih.gov/gene/851152 NCBI Gene Database:]
**[https://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YLR432W;r=XII:1002557-1004128;t=YLR432W_mRNA Ensembl:]
**[https://www.uniprot.org/uniprotkb/P50095/entry UniProt:]
*What is the DNA sequence of your gene?
**ATGGCCGCCGTTAGAGACTACAAGACTGCCTTGGAATTCGCCAAGAGCTTACCAAGACTAGATGGTTTGTCTGTCCAGGAGTTGATGGACTCCAAGACCAGAGGTGGGTTGACTTATAACGACTTTTTGGTTTTGCCAGGTCTGGTTGATTTCCCATCTTCTGAAGTTAGCCTACAAACTAAGTTGACAAGGAATATCACTTTGAACACCCCATTCGTTTCCTCTCCAATGGACACCGTGACAGAATCAGAAATGGCCATCTTCATGGCTTTGTTGGGTGGTATCGGTTTTATTCACCACAACTGTACCCCAGAGGACCAAGCTGACATGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCCCCAACTACTACTGTGGGTGAAGCTAAGAGTATGAAGGAAAGATTTGGATTTTCCGGTTTCCCCGTTACAGAAGATGGTAAAAGAAACGGAAAATTGATGGGTATCGTCACTTCTCGTGATATTCAGTTCGTTGAAGACAACTCTTTGCTTGTTCAAGATGTTATGACCAAAAACCCTGTCACCGGTGCACAAGGTATTACATTGTCTGAAGGTAATGAAATTTTAAAGAAGATTAAAAAGGGTAAGCTATTGATTGTTGACGACAATGGTAACTTAGTTTCTATGCTTTCCAGAACTGATTTAATGAAAAATCAGAACTATCCATTGGCTTCTAAATCTGCCACCACCAAGCAACTGTTATGTGGTGCTGCTATCGGTACTATCGATGCTGATAAGGAAAGGTTAAGACTATTAGTCGAAGCAGGTTTGGATGTTGTTATCTTAGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACATGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGCCACCAGAGAACAAGCTGCTAACTTGATTGCTGCCGGTGCCGATGGTTTAAGAATTGGTATGGGTTCAGGCTCTATTTGTATCACTCAAGAAGTTATGGCCTGTGGTAGACCACAAGGTACAGCCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTATTCCATGTATGGCTGATGGTGGTGTTCAAAACATTGGTCATATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTTATGATGGGTGGTATGTTAGCTGGTACTACTGAATCTCCTGGTGAATATTTCTATCAAGATGGTAAAAGATTGAAGGCATATCGTGGTATGGGTTCCATTGACGCCATGCAAAAGACTGGTACTAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCACAAGGTGTCTCCGGTGCTGTCGTTGACAAAGGTTCTATCAAGAAATTTATTCCATATTTGTACAACGGTTTACAACATTCTTGTCAAGACATTGGTTACAAGTCCCTAACTTTATTAAAGGAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTTAGAACCGCTTCTGCTCAACTAGAAGGTGGTGTTCATAACTTACATTCTTACGAAAAGCGTTTACATAACTAA

*What is the protein sequence corresponding to your gene?
[[Image:IMD3 ExPasy.png|700px]]

Reading frame 1 encodes the IMD3 protein sequence:

MAAVRDYKTALEFAKSLPRLDGLSVQELMDSKTRGGLTYNDFLVLPGLVD
FPSSEVSLQTKLTRNITLNTPFVSSPMDTVTESEMAIFMALLGGIGFIHH
NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKERFGFSGFP
VTEDGKRNGKLMGIVTSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG
NEILKKIKKGKLLIVDDNGNLVSMLSRTDLMKNQNYPLASKSATTKQLLC
GAAIGTIDADKERLRLLVEAGLDVVILDSSQGNSIFQLNMIKWIKETFPD
LEIIAGNVATREQAANLIAAGADGLRIGMGSGSICITQEVMACGRPQGTA
VYNVCEFANQFGIPCMADGGVQNIGHITKALALGSSTVMMGGMLAGTTES
PGEYFYQDGKRLKAYRGMGSIDAMQKTGTKGNASTSRYFSESDSVLVAQG
VSGAVVDKGSIKKFIPYLYNGLQHSCQDIGYKSLTLLKENVQSGKVRFEF
RTASAQLEGGVHNLHSYEKRLHN-
*What is the function of your gene?
**The molecular function of IMD3 is that it enables IMP dehydrogenase activity as well as mRNA binding. It catalyzes the rate-limiting step in the de novo synthesis of GTP and its involved in GTP biosynthesis pathways. In addition, it catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP). It is also known to play an important roll in cell growth.
*What was different about the information provided about your gene in each of the parent databases?
***SDG and Uniprot both provide a variety of in-depth information about the gene. The contents of their information is fairly similar, in particular UniProt has more visual images and charts/graphs compared to SDG. e!Ensemble contains generic information that just covers the basics such as a name, description and type.
**Were there differences in content, the information or data itself?
***There were some differences in content, e!Ensemble didn’t really provide any information on the gene that would help one learn about it. On the other hand UniProt has a lot of information that could be useful for a person studying the gene
***Information across all of the four databases was similar in the way they convey information. Mostly by separating things into sections and using visuals when necessary.
**Were there differences in presentation of the information?
*Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
**Hailey’s research in Dr. Sarah Mitchell’s lab at LMU studies IMD3’s RNA binding function in yeast.
*Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
[[Image:Firstglance imd3.png]]