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remotes::install_github(
"bhklab/AnnotationGx",
build_manual=TRUE,
build_vignettes=TRUE
)
Downloading GitHub repo bhklab/AnnotationGx@HEAD
These packages have more recent versions avai…
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As noted by @andrewsu, GTOPDB:836 is showing up as a SmallMolecule, (it's coming that way out of automat, but that's because NN is tagging that entity as a SmallMolecule).
It looks like we're calli…
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From https://wiki.openphacts.org/index.php/SureChEMBL
> Compounds are assigned SureChEMBL identifiers as used in the SureChEMBL interface and download files. Please note these identifiers have no rel…
stain updated
8 years ago
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This is just to remind us that the links in wikipedia need to be updated to those on the new interface
e.g. https://en.wikipedia.org/wiki/Sildenafil. needs to point to the new version of this:
ht…
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Broken off from RTXteam/RTX-KG2#3:
`match (n)-[r:`biolink:same_as`]->(m) where n.category m.category return distinct r.provided_by, count (r) order by count (r) desc`
r.provided_by | count (r…
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We have 2 different "Cisplatin" entries in Babel/NN.
A main entry: https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PUBCHEM.COMPOUND%3A5460033&conflate=true
And then thi…
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Not really an issue, just a question I couldn't find the answer to in the docs.
What nomenclature or ontology is used to name compounds in the CMap and LINCS L1000 PharmacoSets and perturbation sig…
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In the flat file the substances are only provided via their names. To my knowledge no name to brenda ligand or chebi mapping file exists which could be used for resolving the information.
It is neces…
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This KEGG reaction should be retrieved, as far as I can tell, but we don't have relationships coming from GBA to anything but water (in robokopdb1). Could be a problem with the crawl or with the cli…
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From @saramsey:
> Erica, do you know why the following triple in KG2.8.4pre doesn't have any qualified_object_direction property?
```
match (n {id: 'CHEMBL.COMPOUND:CHEMBL254219'})-[r]->(m {id: 'NC…