Name
   - Human cancer (CDO slim) to tissue ontology (Uberon) mapping

Version
   - 1.0.36

Created on
  - 2019-04-26T15:26:38.719704

Modified on
   - 2021-04-09T13:15:48.608620

Created by
   - Nikhita Gogate [nikigogate@gwu.edu], Hayley Dingerdissen [hmhamilt@gwmail.gwu.edu], Evan Holmes [evanh@gwmail.gwu.edu], Edmund Cauley [escauley@gwu.edu]

Authors
   - 

Checksum
   - 76bfd29738d0a3e3b821844e3be6ead0

Usability Domain
   - Human Cancer Disease Ontology Slim IDs (V2.1) directly mapped to UBERON Anatomical Entity IDs - The csv file human_doid_uberon_mapping.csv contains slim-level Disease Ontology IDs (DOIDs) from the Cancer DO Slim project mapped to the corresponding tissue in the UBERON Anatomical Entity Ontology.

Description Domain
   Keywords
   - DOID
   - CDO slim
   - ontology
   - UBERON
   - cancer
   - normal

   Pipeline Steps
   - Step-1: The file CancerDOSlim2.1_local_HMD_5Sep2018.xlsx (not in server) was filtered to remove terms "DOID:305 / carcinoma" and "DOID:0070003 / blastoma"
   - Step-2: Interim file was then altered such that term "DOID:3963 / thyroid carcinoma" was changed to "DOID:1781 / thryoid cancer" and term "DOID:3119 / gastrointestinal system cancer" was changed to "DOID:9253 / gastrointestinal stromal tumor"
   - Step-3: Remaining DOIDs were mapped manually to corresponding UBERON Anatomical Entity ID using the current DO owl file doid.owl (in server)
   - Step-4: UBERON Anatomical Entity names were manually retrieved by querying the corresponding UBERON ID at ontobee.org
   - Step-5: Resulting information was output in human_doid_slim_uberon_mapping.csv

Execution Domain
   Scripts

   Software Prerequisites

I/O Domain
   Output Subdomain
      Name: human_cdo_slim_uberon_mapping.csv
      URI: http://data.oncomx.org/ln2wwwdata/reviewed/human_cdo_slim_uberon_mapping.csv
      Name: human_cdo_slim_uberon_mapping.stat.csv
      URI: http://data.oncomx.org/ln2wwwdata/reviewed/human_cdo_slim_uberon_mapping.stat.csv

Fields
      Name: "uberon_anatomical_id"
     Description: "Uberon anatomical entity identifier"
      Unique Values: "53"
      Name: "uberon_anatomical_entity_syn"
     Description: "Anatomical term summarizing uberon anatomical entity"
      Unique Values: "13"
      Name: "uberon_anatomical_name"
     Description: "Uberon anatomical entity name corresponding to an uberon anatomical entity id"
      Unique Values: "52"
      Name: "do_full"
     Description: "Composite field combining DOID
      Unique Values: "76"