Andrew Su
Andrew Su
UMLS is a key biomedical resource for genes and other entities. http://mygene.info/v3/metadata says the last update was April 2020. According to the [release history](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html), UMLS is updated twice a year...
The Alliance of Genome Resources (AGR) is a consortium of the most highly-used model organisms (mouse, rat, worm, fly, zebrafish, yeast), and they have released their own set of ortholog...
The FDA provides [Unique Ingredient Identifiers (UNII)](https://en.wikipedia.org/wiki/Unique_Ingredient_Identifier), primarily for small molecule compounds but also for the proteins that they target. The complete list of UNIIs for proteins with mappings to...
"The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body" (from https://hmdb.ca/). HMDB contains links between proteins...
In https://github.com/biothings/mygene.info/blob/master/src/hub/dataload/sources/clingen/parser.py#L65 of the current clingen parser, we specify five columns to parse out of the downloaded clingen file `key_list = ['DISEASE LABEL', 'DISEASE ID (MONDO)', 'SOP', 'CLASSIFICATION', 'ONLINE REPORT']`...
Orphanet provides gene-disease associations for rare diseases under at CC-BY 4.0 license. See link for "Genes associated with rare diseases" in http://www.orphadata.org/cgi-bin/index.php. Current XML file appears to be continuously updated...
Per #103, we can do a fielded search for MGI IDs by simply escaping the colon in the CURIE. This strategy also works for GO IDs, but not MONDO IDs:...
I can query for genes with an explicit annotation for a GO term, e.g., http://mygene.info/v3/query?q=GO:0061702 However, `GO:0061702` [has four children](http://amigo.geneontology.org/amigo/term/GO:0061702#display-lineage-tab) -- `GO:0097169`, `GO:0072557`, `GO:0072558`, and `GO:0072559`. Is there an easy...