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biothings / biothings_explorer_web_old

Web Interface for BioThings Explorer
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Add more Data Sources in BT Explorer 1.0 version #36

Closed kevinxin90 closed 6 years ago

kevinxin90 commented 6 years ago
  1. Reactome
  2. Pharos
  3. Chembl (more endpoints)
  4. GeneProf
  5. NCBI eUtils (more endpoints)
kevinxin90 commented 6 years ago

Parser from RTX team for Chembl: https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/QueryChEMBL.py They only use two of the endpoints from Chembl: 1.compound_record -> convert from drug name to chembl id 2.target_prediction -> get predicted protein targets for a chembl id

kevinxin90 commented 6 years ago

Parser from RTX team for Pharos: https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/QueryPharos.py Endpoints used

  1. /disease/search -> convert from disease name to pharos disease id
  2. /ligand/search -> convert from drug name to pharos ligand id
  3. /target(targetid) a. -> get relationship between pharos target id and disease b. -> get relationship between pharos target and ligand
  4. /ligand(ligandid) a. -> get relationship between pharos ligand id and target
kevinxin90 commented 6 years ago

Parser from RTX team for Disease Ontology:https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/QueryDisont.py Endpoint used:

  1. /do We need to add JSON-LD context for fetching DO parent, children, and disease name
kevinxin90 commented 6 years ago

Parser from RTX team for Reactome: https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/QueryReactome.py Endpoint used

  1. data/complexes/UniProt: -> uniprot to reactome entity id
  2. data/pathways/low/diagram/entity: -> reactome entity id to reactome pathway id
  3. data/participants: -> reactome pathway id to uniprot id
  4. interactors/static/molecule: -> uniprot id -> interacting uniprot id
kevinxin90 commented 6 years ago

Parser from RTX team for GeneProf: https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/QueryGeneProf.py Endpoint used:

  1. gene.info/gp.id: -> gene symbol to geneprof id
  2. gene.info/regulation/bionary/by.target: -> geneprof id to TF factor
kevinxin90 commented 6 years ago

Parser from RTX team for PathwayCommons2:https://github.com/RTXteam/RTX/blob/master/code/reasoningtool/QueryPC2.py Endpoint used

  1. reactome to uniprot
  2. uniprot to reactome pathway id