30 minutes x 5 biomolecular databases

Published: 2021-08-18

During the autumn term, the library will hold five 30-minute lunchtime presentations (in Zoom) on open science databases (often called knowledge bases) with biomolecular content. The presentations are intended for doctoral students and researchers in pre-clinical and translational research.

First up is MarkerDB which is a comprehensive database of about 28,000 molecular biomarkers: chemical, genetic, protein and karyotypic. In the database, detailed descriptions of the markers themselves as well their associated conditions/diseases are found. MarkerDB can therefore be used to find a biomarker for a specific medical condition or disease.

Then comes Alliance of Genome Resources which was recommended by the Journal of Nucleic Acid (NAR) database edition 2020 as a “breakthrough” database. The journal editors believe that the database will have a strong impact on the research community. Alliance of Genome Resources can be used to make biomolecular comparisons between human and model organism species.

Followed by Monarch Initiative which was also recommended in an earlier volume of the NAR journal. The database can be used to make phenotypic comparisons across multiple species. It can also be used to identify medical conditions with similar phenotypic profiles.

Next comes Simple ClinVar which was recommended in database Faculty Opinions. Simple ClinVar is actually a web server which gives an easier and more intuitive visualization of the data in ClinVar (the largest publicly available genetic variant database). It can be used to find a genetic mutation causing disease. 

Finally, this term, Europe PubMed Central (PMC) and BioStudies will be presented. These are ELIXIR databases. Europe PMC contains bibliographic records and Open Access full text articles which have been text-mined to highlight key concepts and link to other data sources. Europe PMC is also linked to BioStudies that contains supplementary research data and is a one-stop-shop for all information about a study.

All the databases are relatively new and are often being developed with a user-experience (UX) approach. The databases are also examples of how open data can be reused and mixed together to create new sources of knowledge.

The presentations are intended for doctoral students and researchers in pre-clinical and translational research at KI. You register via each event in our calendar. A Zoom link will be sent to you closer to the presentation.