30 ms·

What are some other good scientific databases compiled from the open literature? Are there any best practices for the construction of similar databases?

mkhorton 6y ago
For crystallography specifically, there's ourselves (Materials Project), OQMD, AFLOW, Materials Cloud, JARVIS, and a number of more specific (but no less important) specialized databases. There are also a number of commercial offerings. Best practices are incredibly difficult. We're trying to establish a common API currently (https://github.com/Materials-Consortia/optimade https://github.com/Materials-Consortia/optimade) that can be adopted by all database providers. How the data is stored behind the scenes is something that ends up being very specific to how the data is generated and what its applications are. We're definitely better as a community than we were ten years ago, but there's a lot of work to be done here. In terms of scientific databases outside crystallography/materials science, Nature's Scientific Data is a good open-access journal to peruse: https://www.nature.com/sdata/ https://www.nature.com/sdata/
jszymborski 6y ago
NCBI's Gene Expression Omnibus (GEO) for bulk and single-cell RNA sequencing https://www.ncbi.nlm.nih.gov/geo/ https://www.ncbi.nlm.nih.gov/geo/ The Cancer Genome Atlas (TCGA) for a wide-array of data from cancer patients in the US (Treatment history, outcomes, histology, expression, etc) https://portal.gdc.cancer.gov/ https://portal.gdc.cancer.gov/ InterPro from EMBL harmonizes multiple protein family databases https://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/ STRING harmonizes protein-protein interaction databases https://string-db.org/ https://string-db.org/
ylem 6y ago
There's the classic, Protein Data Bank. A number of people in the field saw it as a moral imperative. It's interesting how open different disciplines are to openness

mkhorton 6y ago

For crystallography specifically, there's ourselves (Materials Project), OQMD, AFLOW, Materials Cloud, JARVIS, and a number of more specific (but no less important) specialized databases. There are also a number of commercial offerings. Best practices are incredibly difficult. We're trying to establish a common API currently (https://github.com/Materials-Consortia/optimade https://github.com/Materials-Consortia/optimade) that can be adopted by all database providers. How the data is stored behind the scenes is something that ends up being very specific to how the data is generated and what its applications are. We're definitely better as a community than we were ten years ago, but there's a lot of work to be done here. In terms of scientific databases outside crystallography/materials science, Nature's Scientific Data is a good open-access journal to peruse: https://www.nature.com/sdata/ https://www.nature.com/sdata/

jszymborski 6y ago

NCBI's Gene Expression Omnibus (GEO) for bulk and single-cell RNA sequencing https://www.ncbi.nlm.nih.gov/geo/ https://www.ncbi.nlm.nih.gov/geo/ The Cancer Genome Atlas (TCGA) for a wide-array of data from cancer patients in the US (Treatment history, outcomes, histology, expression, etc) https://portal.gdc.cancer.gov/ https://portal.gdc.cancer.gov/ InterPro from EMBL harmonizes multiple protein family databases https://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/ STRING harmonizes protein-protein interaction databases https://string-db.org/ https://string-db.org/

ylem 6y ago

There's the classic, Protein Data Bank. A number of people in the field saw it as a moral imperative. It's interesting how open different disciplines are to openness