Difference between revisions of "AgeAnnoMO Week 4"
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=== Is it convenient to browse the data? === | === Is it convenient to browse the data? === | ||
Revision as of 15:43, 6 February 2024
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:
AgeAnnoMo
[[1]]
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")?
It is secondary since they collected the data from previous studies
curated versus non-curated?
Curated
if curated, is it electronic versus human curation?
Human curation because they picked the species and the datasets
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
Multinational entity with contributors being UT health, West China School of Medicine, Xidian University.
What is their funding source(s)?
- ??? Would it be funding from university tuition
Scientific quality of the database:
Does the content appear to completely cover its content domain?
*How many records does the database contain?
136 aging datasets. Do I include 50 species, samples, cells, etc?
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.)
There is 50 species? But when you go brows species there is only 20.
*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?
Is there a need in the scientific community for such a database at this time?
Is the content covered by other databases already?
How current is the database?
The datasets depending on species range back from 2015-2022.
When did the database first go online?
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
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?
The content page to brows 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, it's presented in tiny rows with words half cut off.
Is it convenient to download the data?
In what file formats are the data provided?
What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
Is the website well-organized?
Does it have a help section or tutorial?
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.
