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Some protein nodes are missing descriptions #20
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Found another such node:
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confirmed this bug in the current dev KG (in container rtxsteve on rtxdev.saramsey.org) |
Confirmed fixed in http://rtxsteve.saramsey.org:7474 |
Working on copying the Neo4j database to the less-expensive "rtxdev" EC2 instance now.... |
Updated database has been pushed to http://rtxdev.saramsey.org:7674 |
Note also that some of the target edges are missing probabilities:
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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.edu<mailto: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
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@saramsey Closing the loop on this issue: some of the probabilities are still not populated:
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. |
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.edu<mailto: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:
@saramsey<https://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.
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Fair enough: let's chalk it up to a shortcoming of the KS's. Guess we can close this issue then. |
Eg. P08563
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