AgeAnnoMO Week 4
Contents
- 1 AgeAnnoMo
- 2 General information about the database
- 2.1 What is the name of the database? (link to the home page)
- 2.2 What type (or types) of database is it?
- 2.3 What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
- 2.4 What type of data source does it have?
- 2.5 Primary versus secondary ("meta")?
- 2.6 curated versus non-curated?
- 2.7 if curated, is it electronic versus human curation?
- 2.8 if human curation, is it in-house staff versus community curation?
- 2.9 What individual or organization maintains the database?
- 2.10 Public versus private?
- 2.11 Large national or multinational entity or small lab group
- 2.12 What is their funding source(s)?
- 3 Scientific quality of the database:
- 3.1 Does the content appear to completely cover its content domain?
- 3.2 *How many records does the database contain?
- 3.3 What claims do the database owners make about coverage in the corresponding paper?
- 3.4 *What species are covered in the database? (If it is a very long list, summarize.)
- 3.5 *Is the database content useful? I.e., what biological questions can it be used to answer?
- 3.6 Is the database content timely?
- 3.7 Is there a need in the scientific community for such a database at this time?
- 3.8 Is the content covered by other databases already?
- 3.9 How current is the database?
- 3.10 When did the database first go online?
- 3.11 How often is the database updated?
- 3.12 When was the last update?
- 3.13 General utility of the database to the scientific community
- 3.14 Are there links to other databases? Which ones?
- 3.15 Is it convenient to browse the data?
- 3.16 Is it convenient to download the data?
- 3.17 In what file formats are the data provided?
- 3.18 What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
- 3.19 Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
- 3.20 Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
- 3.21 Is the website well-organized?
- 3.22 Does it have a help section or tutorial?
- 3.23 Are the search options sensible?
- 3.24 Run a sample query. Do the results make sense?
- 3.25 Access: Is there a license agreement or any restrictions on access to the database?
- 4 Summary judgment:
- 5 Presentation
- 6 References:
- 7 Acknowledgements:
AgeAnnoMo
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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.
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.
