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Pathway Figure OCR (PFOCR)
Anders Riutta edited this page Apr 30, 2021
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Pathway Figure OCR (PFOCR) is a collection of gene sets extracted from biological pathway figures published in the scientific literature. PFOCR is available as an API in BTE and via a Shiny app (wait a bit for it to load).
- TRAPI endpoint: https://api.bte.ncats.io/v1/query/
- Smart API Registry link: https://smart-api.info/registry?q=edeb26858bd27d0322af93e7a9e08761
Use Cases - PFOCR adds entities, links and context for various query paths in BTE. See https://github.com/NCATSTranslator/testing/ for example tests.
- Query demo: https://biothings.ncats.io/pfocr
Knowledge Providers Accessed - PFOCR is a source of knowledge itself and will also be used to rank/sort paths in BTE and may be adaptable to other ARAs and/or applications). As part of PFOCR's construction, it accesses the following sources:
- PubMed Central https://www.ncbi.nlm.nih.gov/pmc/
- PubTator https://www.ncbi.nlm.nih.gov/research/pubtator/
- HGNC https://www.genenames.org/
Source Code
- All source code is in https://github.com/wikipathways/pathway-figure-ocr
External Documentation
- Codebook and latest paper