Table 1 Resources in PhenCards. Some resources require regular updates and downloads to stay abreast of changes, but the majority of resources are API or web-based and require no changes to stay up-to-date
From: PhenCards: a data resource linking human phenotype information to biomedical knowledge
Resource(s) | Method of access | Update needed? | Content |
|---|---|---|---|
HPO [4, 13] (includes OMIM [3, 21] and Orphanet [2]), Disease Ontology [19, 20] | Elasticsearch [25] on indexed database | Yes, monthly | Standardized phenotype and disease terms |
Elasticsearch on indexed database | Yes, yearly | Standardized phenotype and disease terms | |
Pharos (disease) [30] | API | No | Disease aliases, expression, drug, pathway, Gene Ontology data |
IRS (Internal Revenue Service), Open990 | Elasticsearch on indexed database | Yes, yearly | Nonprofit grants and foundations |
NIH (National Institute of Health) Federal Reporter, NIH FOAs (funding opportunity announcements) | API | No | Federal grant and projects |
Direct2Experts [31] | API | No | Collaborators, specialty physicians |
openFDA [32], Tocris, APExBio, Pharos (target) [30], DrugCentral [33] | API | No | Federal and company drug, drug target and adverse effect data |
API | No | Pathways: diseases, biological functions | |
API | No | Clinical trials: studies, procedures, drugs | |
Columbia Open Health Data [36] | API | No | Co-occurring patient drug, procedure, and condition terms |
Doc2Hpo [37] | API | No | NLP algorithm for optimally extracting terms from text |
Phen2Gene [38] | API | No | Algorithm ranking candidate genes for a set of HPO terms |
PubMed [39] | API | No | Biomedical literature |
Google Scholar | API | No | Large-scale scholarly search engine |