Some protein nodes are missing descriptions

[dkoslicki]

Eg. P08563

[dkoslicki]

Found another such node:

match (n) where n.name="DOID:10923" return n

[saramsey]

confirmed this bug in the current dev KG (in container rtxsteve on rtxdev.saramsey.org)

[saramsey]

Confirmed fixed in http://rtxsteve.saramsey.org:7474

[saramsey]

Working on copying the Neo4j database to the less-expensive "rtxdev" EC2 instance now....

[saramsey]

Updated database has been pushed to http://rtxdev.saramsey.org:7674

[saramsey]

all drugs now have descriptions:

[saramsey]

Looks like 303 protein nodes lack descriptions. Not clear from a search of the code-base where these are coming from. More investigation needed:

[dkoslicki]

Note also that some of the target edges are missing probabilities:

match p=(n:pharos_drug)-[t:targets]-(:uniprot_protein) return t.probability limit 10

t.probability
--
null
null
null
0.03231776208
0.00615026285
7.3254e-7
1
0.00000596881
0.00000803035
0.00000190193

[saramsey]

Can you give me a pair of ChEMBL ID and Uniprot ID?

---

Stephen Ramsey Assistant Professor, Oregon State University

• School of Electrical Engineering and Computer Science
• Department of Biomedical Sciences 208A Dryden Hall stephen.ramsey@oregonstate.edumailto:stephen.ramsey@oregonstate.edu http://lab.saramsey.org

On Mar 29, 2018, at 3:17 PM, David Koslicki notifications@github.com<mailto:notifications@github.com> wrote:

Note also that some of the target edges are missing probabilities:

match p=(n:pharos_drug)-[t:targets]-(:uniprot_protein) return t.probability limit 10

t.probability

null null null 0.03231776208 0.00615026285 7.3254e-7 1 0.00000596881 0.00000803035 0.00000190193

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/RTXteam/RTX/issues/20#issuecomment-377389503, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFTe-9kVeXFSITYGsFmyQ3ro-0enYCUNks5tjV13gaJpZM4SlFJL.

[dkoslicki]

MATCH p=(s:pharos_drug)-[r:targets]->(t:uniprot_protein) where r.probability is Null return s.name, t.name, r.probability limit 10

s.name | t.name | r.probability
-- | -- | --
"CHEMBL1166" | "Q9H244" | null
"CHEMBL1166" | "Q9BQB6" | null
"CHEMBL1166" | "P03952" | null
"CHEMBL1166" | "P38435" | null
"CHEMBL1201244" | "P02708" | null
"CHEMBL1201244" | "P11230" | null
"CHEMBL1201244" | "Q07001" | null
"CHEMBL1201244" | "P08913" | null
"CHEMBL602" | "P13569" | null
"CHEMBL602" | "P37231" | null

[dkoslicki]

@saramsey Closing the loop on this issue: some of the probabilities are still not populated:

match p=(n:chemical_substance)-[t:directly_interacts_with]-(m:protein) where not exists(t.probability) return t.probability, n.description, m.description limit 100

eg edge connecting triclofos and GABRE.

If this is due to Pharos not having the info, then it's fine and we can close this issue. I just wanted to make sure it wasn't a problem with the orangeboard construction itself.

[saramsey]

Yes, this is a Pharos issue (see screen cap). Since we first attempt to get drug-target relationships using ChEMBL before attempting Pharos, not sure what else can be done here.

[cid:F794E69F-2503-471B-86CC-A856E430B859]

---

Stephen Ramsey Assistant Professor, Oregon State University

• School of Electrical Engineering and Computer Science
• Department of Biomedical Sciences 208A Dryden Hall stephen.ramsey@oregonstate.edumailto:stephen.ramsey@oregonstate.edu http://lab.saramsey.org

On Apr 16, 2018, at 2:22 PM, David Koslicki notifications@github.com<mailto:notifications@github.com> wrote:

@saramseyhttps://github.com/saramsey Closing the loop on this issue: some of the probabilities are still not populated:

match p=(n:chemical_substance)-[t:directly_interacts_with]-(m:protein) where not exists(t.probability) return t.probability, n.description, m.description limit 100

eg edge connecting triclofos and GABRE.

If this is due to Pharos not having the info, then it's fine and we can close this issue. I just wanted to make sure it wasn't a problem with the orangeboard construction itself.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/RTXteam/RTX/issues/20#issuecomment-381754054, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFTe-y_xdfyGpBo59xJgkLIOvxk2TMvJks5tpQuMgaJpZM4SlFJL.

[dkoslicki]

Fair enough: let's chalk it up to a shortcoming of the KS's. Guess we can close this issue then.