BIOL368/S20:Sahil Patel Week 10

Purpose

The purpose of this assignment is to critically evaluate a biological database while developing and using assessment techniques unique to scientists.

Database Evaluation

General information about the database
1. What is the name of the database? [Biomodels Homepage]
2. What type (or types) of database is it?
  1. What biological information (type of data) does it contain? BioModels Database is a repository of computational models of biological processes. [Biomodels Homepage]
  2. What type of data source does it have?
    - primary versus secondary ("meta")? Secondary
    - curated versus non-curated? Both curated and non-curated [Biomodels Homepage]
      - if curated, is it electronic versus human curation? These models are manually curated and semantically enriched with cross-references to external data resources (such as publications, databases of compounds and pathways, ontologies, etc.) [FAQ]
3. What individual or organization maintains the database? European Molecular Biology Laboratory [Biomodels Homepage]
  - public [Biomodels Homepage]
  - medium sized multinational entity [Biomodels Homepage]
4. What is their funding source(s)? Most funding comes from EMBL member states: Austria, Belgium, Croatia, Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Israel, Italy, Lithuania, Luxembourg, Malta, Montenegro, The Netherlands, Norway, Portugal, Slovakia, Spain, Sweden, Switzerland, United Kingdom. As well as, EMBL associate member states: Argentina, Australia. Other major funders include the European Commission, the US National Institutes of Health, the Wellcome Trust, UK Research Councils and members of our Industry Programme. [FAQ]

Scientific quality of the database
1. Does the content appear to completely cover its content domain? Yes, after thoroughly exploring the BioModels Database website, I believe that the content domain has been covered but not saturated and is still a growing repository. [FAQ]
  - How many records does the database contain? Of the manually curated there are 3 Logical and 650 ODE and for the Non curated there are 10 Logical, 452 Constraint based, and 561 ODE. [Biomodels Homepage]
  - What claims do the database owners make about coverage in the corresponding paper? It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. [Biomodels Homepage]
2. What species are covered in the database? Humans, Mouse, and Yeast. [[1]]
3. Is the database content useful? I.e., what biological questions can it be used to answer? BioModels contains quantitative information representing the quantities (amount or concentration of species) or kinetics in a model. [FAQ]
4. Is the database content timely? Yes it is very timely.[FAQ]
  - Is there a need in the scientific community for such a database at this time? Yes, , it allows users to carry out simulations where a model produces quantitative results with the available experimental knowledge.[FAQ]
  - Is the content covered by other databases already? BioModels has its own controlled annotation and vocabulary which allows users to search not only for particular models based on their internal components elements, and extensive additional annotation added to the model through manual curation. These annotations increase access and visibility, both for the model and relevant resources linked to the model on BioModels, thereby facilitating the understanding of the concepts upon which the model is founded. [FAQ]
5. How current is the database? It is very current, in fact a new platform has just been designed and released. [About us]
  - When did the database first go online? April 2005 [About us]
  - How often is the database updated? Bi-weekly [About us]
  - When was the last update? March 18, 2020 [Biomodels Homepage]

General utility of the database to the scientific community
1. Are there links to other databases? Which ones? Ensembl, Uniprot, PDBe, Europe PMC, Expression Atlas, ChEMBL [Database Collabs]
2. Is it convenient to browse the data? Yes, easy to filter through data as well [Data]
3. Is it convenient to download the data? Yes free convenient access [Data]
  - In what file formats are the data provided? The data is provided in SBML format and a few in original MATLAB code [Data]
    - What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? .xml [Data]
    - Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)? standard format [Data]
4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information? on a scale of 1-10: 6 [Data]
  - Is the website well-organized? Website is pretty well organized. Easy to find things. [[2]]
  - Does it have a help section or tutorial? It has a FAQ page that is quite good and also has an email provided for further questions. [FAQ]
  - Are the search options sensible? Yes [Data]
  - Run a sample query. Do the results make sense? Yes, good algorithm for keywords. [Data]
5. Access: Is there a license agreement or any restrictions on access to the database? No, all the information is reproducible and freely-accessible for the public [FAQ]

Summary judgment
1. Would you direct a colleague unfamiliar with the field to use it? If a colleague needed to find quantitative models for biological contexts then I would definitely direct them to this database.
2. Is this a professional or "hobby" database? This is a professional database run by a multinational laboratory.

Conclusion

The BioModels Database has provided the public domain with mathematical models of biological and biomedical systems. After exploring and evaluating this database from the lens of a biologist, I would say that it clearly meets the criteria for a credible and reliable source and I would definitely recommend it for those interested in biomathematical modeling.

Acknowledgments

I would like to thank our peer, Christina Dominguez for helping answer many of our questions with this assignment.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

References

BioModels. (2020). Biomodels. Retrieved April 1, 2020, from https://www.ebi.ac.uk/biomodels/
OpenWetWare. (2020). BIOL368/S20:Week 10. Retrieved March 26, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_10.