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Chemical compound databases
- Evan Bolton
- Chihiro Higuchi https://orcid.org/0000-0003-2808-2813
- Tatsuya Kushida
- Yuka Tateisi https://orcid.org/0000-0002-3813-5782
- Tetsuo Katsuragi
- Hideki Hatanaka https://orcid.org/0000-0002-0587-2460
- RDFization of DruMAP (drug metabolism/pharmacokinetics database)
- Nikkaji (chemical compound dictionary (ja/en))
- Its RDF has changed as the provider
The working group has a plan...
DruMAP is drug metabolism / pharmacokinetics database developped by National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN). It works on https://drumap.nibiohn.go.jp/ currently. In this time, we carried out RDFization of DruMAP database to integrate NBDC RDF portal for advanced analysis. In this RDFization, we selected suitable URIs with reference to the notation of PubChem RDF. This hackathon’s goal is to complete the RDF schema diagram.
We have obtained the specification of Nikkaji RDF, and have developed a python script to convert the original Nikkaji (in JSON format) to RDF format. We tested the script on a portion of Nikkaji JSON data and confirmed that the output is in accordance with the specification. In the process of testing, we found many tricky structures, for example, LISP-like lists of compound names. We decided to discard the structure and order information of names for easier searching of names. We defined a newly created schema in the form of a schema diagram.
We also compared Nikkaji and PubChem and found non 1-to-1 correspondence. The list of such entries were shared, and the inconsistencies were classified.
- The first group (“2 or 3 Nikkaji entries for a CID”) were investigated. They are stereoisomers, so either Nikkaji entry should link to another CID. A problem is that cis/trans ambiguity is not represented in Nikkaji MOL files.
- The second group (“2 Nikkaji entries for a structure”) and the third (“2 Nikkaji entries have the same name”) will be handed to the Nikkaji curators.
The working group made a solution for the problem.
Future!