Import all AOP-Wiki stressor

[marvinm2]

This SPARQL query for all chemicals in AOP-Wiki (with related stressor ID and InChIkey): https://edu.nl/nbcar

[egonw]

I used this SPARQL in the end, as input for my tools, and the rest is described at https://compoundcloud.wikibase.cloud/wiki/User:Egonw/AOP

SELECT (substr(str(?inchikey), 34) as ?inchikey1)
       (substr(str(?Stressor), 38) as ?stressor1)       
       ?chemicalname
WHERE{
?Stressor aopo:has_chemical_entity ?Chemical.
?Chemical dc:title ?chemicalname ; cheminf:000059 ?inchikey  .
}

[egonw]

First batch of 255 is pushed, 4 failed. This is out of 381 starting rows from the SPARQL.

• 26 already in our wiki: grep "^#" results.txt | grep "already in VHP4Safety Compounds" | wc -l
• 38 records with multiple SMILES: grep "^#" results.txt | grep "Multiple SMILES" | wc
• 62 records that do not seem to be in PubChem (wrong InChIKey?): grep "^#" results.txt | grep "Error while downloading from URL" | wc -l

[egonw]

Four failed because they had a label we already had in our Wiki (wrong InChIKey?)

[egonw]

I just need to match InChIKey with 26 already existing in our wiki, if they do have their InChIKey already

[egonw]

@marvinm2, this is the list of InChIKeys not found in PubChem, apparently. We should explore that at some point:

# DYKFCLLONBREIL-KVUCHLLUSA-N exception: Error while downloading from URL.
# CLPFFLWZZBQMAO-UHFFFAOYNA-N exception: Error while downloading from URL.
# CLPFFLWZZBQMAO-UHFFFAOYNA-N exception: Error while downloading from URL.
# LUTPDAWYUNZUTI-BQTIBMHRSA-N exception: Error while downloading from URL.
# PXMNMQRDXWABCY-UHFFFAOYNA-N exception: Error while downloading from URL.
# LQDARGUHUSPFNL-UHFFFAOYNA-N exception: Error while downloading from URL.
# RDYMFSUJUZBWLH-UHFFFAOYNA-N exception: Error while downloading from URL.
# UGFHIPBXIWJXNA-UHFFFAOYNA-N exception: Error while downloading from URL.
# BJQHLKABXJIVAM-UHFFFAOYNA-N exception: Error while downloading from URL.
# BJQHLKABXJIVAM-UHFFFAOYNA-N exception: Error while downloading from URL.
# ZOCSXAVNDGMNBV-UHFFFAOYNA-N exception: Error while downloading from URL.
# PPDBOQMNKNNODG-UHFFFAOYNA-N exception: Error while downloading from URL.
# LDVVMCZRFWMZSG-UHFFFAOYNA-N exception: Error while downloading from URL.
# ZMYFCFLJBGAQRS-UHFFFAOYNA-N exception: Error while downloading from URL.
# JPGQOUSTVILISH-UHFFFAOYNA-N exception: Error while downloading from URL.
# BCQZXOMGPXTTIC-UHFFFAOYNA-N exception: Error while downloading from URL.
# HEFNNWSXXWATRW-UHFFFAOYNA-N exception: Error while downloading from URL.
# UBDNTYUBJLXUNN-IFLJXUKPSA-N exception: Error while downloading from URL.
# DKYWVDODHFEZIM-UHFFFAOYNA-N exception: Error while downloading from URL.
# BYBLEWFAAKGYCD-UHFFFAOYNA-N exception: Error while downloading from URL.
# JHRWWRDRBPCWTF-UHFFFAOYNA-N exception: Error while downloading from URL.
# PIWKPBJCKXDKJR-UHFFFAOYNA-N exception: Error while downloading from URL.
# DEIGXXQKDWULML-UHFFFAOYNA-N exception: Error while downloading from URL.
# QXJKBPAVAHBARF-UHFFFAOYNA-N exception: Error while downloading from URL.
# NPUKDXXFDDZOKR-UHFFFAOYNA-N exception: Error while downloading from URL.
# GFZBJFWXHCSNPX-HBPAQXCTNA-N exception: Error while downloading from URL.
# UDHXJZHVNHGCEC-UHFFFAOYNA-N exception: Error while downloading from URL.
# XJGBDJOMWKAZJS-UHFFFAOYNA-N exception: Error while downloading from URL.
# MLKXDPUZXIRXEP-MFOYZWKCNA-N exception: Error while downloading from URL.
# PVHUJELLJLJGLN-UHFFFAOYNA-N exception: Error while downloading from URL.
# FZRBKIRIBLNOAM-WHVZTFIZNA-N exception: Error while downloading from URL.
# SUVMJBTUFCVSAD-UHFFFAOYNA-N exception: Error while downloading from URL.
# QKICWELGRMTQCR-UHFFFAOYNA-N exception: Error while downloading from URL.
# FSCWZHGZWWDELK-UHFFFAOYNA-N exception: Error while downloading from URL.
# SGTNSNPWRIOYBX-UHFFFAOYNA-N exception: Error while downloading from URL.
# KPSRODZRAIWAKH-UHFFFAOYNA-N exception: Error while downloading from URL.
# KAATUXNTWXVJKI-UHFFFAOYNA-N exception: Error while downloading from URL.
# RLLPVAHGXHCWKJ-UHFFFAOYNA-N exception: Error while downloading from URL.
# PUXBGTOOZJQSKH-UHFFFAOYNA-N exception: Error while downloading from URL.
# JLYXXMFPNIAWKQ-GNIYUCBRNA-N exception: Error while downloading from URL.
# ULSLJYXHZDTLQK-UHFFFAOYNA-N exception: Error while downloading from URL.
# DFBKLUNHFCTMDC-PICURKEMNA-N exception: Error while downloading from URL.
# STJLVHWMYQXCPB-UHFFFAOYNA-N exception: Error while downloading from URL.
# VKQFCGNPDRICFG-UHFFFAOYNA-N exception: Error while downloading from URL.
# ZDOOQPFIGYHZFV-UHFFFAOYNA-N exception: Error while downloading from URL.
# QXHHHPZILQDDPS-UHFFFAOYNA-N exception: Error while downloading from URL.
# UIAGMCDKSXEBJQ-UHFFFAOYNA-N exception: Error while downloading from URL.
# QQODLKZGRKWIFG-UHFFFAOYNA-N exception: Error while downloading from URL.
# RZTAMFZIAATZDJ-UHFFFAOYNA-N exception: Error while downloading from URL.
# FRCCEHPWNOQAEU-UHFFFAOYNA-N exception: Error while downloading from URL.
# RMOGWMIKYWRTKW-DUXBJXIBNA-N exception: Error while downloading from URL.
# PJVWKTKQMONHTI-UHFFFAOYNA-N exception: Error while downloading from URL.
# DEKWZWCFHUABHE-UHFFFAOYNA-N exception: Error while downloading from URL.
# OMFRMAHOUUJSGP-KLUXTTGUNA-N exception: Error while downloading from URL.
# OWZPCEFYPSAJFR-UHFFFAOYNA-N exception: Error while downloading from URL.
# HTIQEAQVCYTUBX-UHFFFAOYNA-N exception: Error while downloading from URL.
# ZXQYGBMAQZUVMI-VGISDWQONA-N exception: Error while downloading from URL.
# NHDHVHZZCFYRSB-UHFFFAOYNA-N exception: Error while downloading from URL.
# GRXKLBBBQUKJJZ-UHFFFAOYNA-N exception: Error while downloading from URL.
# OIRFJRBSRORBCM-UHFFFAOYNA-N exception: Error while downloading from URL.
# GXPHKUHSUJUWKP-UHFFFAOYNA-N exception: Error while downloading from URL.
# XQJQCBDIXRIYRP-UHFFFAOYNA-N exception: Error while downloading from URL.

[egonw]

I just matched another 20 AOP Stressor IDs with entries already in our compound wiki. That completes this round successfully.

[egonw]

Finally, the mashup of VHP compound with AOP-Wiki: https://edu.nl/tc84a