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Knowledge-Graph-Hub / kg-covid-19

An instance of KG Hub to produce a knowledge graph for COVID-19 response.
https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki
BSD 3-Clause "New" or "Revised" License
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SARS-COV-2 <-> human protein interactions from Gordon et al. #31

Closed justaddcoffee closed 4 years ago

justaddcoffee commented 4 years ago

The Gordon et al paper on Biorxiv: https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1

Probably we want supp table 2 (SARS-COV-2 <-> human protein ppi), but lots of other info to ingest here later

SUPPLEMENTARY INFORMATION Supplementary table 1: Scoring results for all baits and all proteins Supplementary table 2: SARS-CoV 2 high confidence interactors Supplementary table 3: Literature-derived drugs and reagents that modulate SARS-Cov-2 interactors. Drugtarget associations drawn from chemoinformatic searches of the literature, including information about purchasability Supplementary table 4: Expert-identified drugs and reagents that modulate SARS-CoV-2 interactors. Drugtarget associations drawn from expert knowledge of human protein interactors of SARS-Co-V2 and reagents and drugs that modulate them; not readily available from the chemoinformatically-searchable literature Supplementary table 5: Raw chemical associations to prey proteins IUPHAR/BPS Guide to Pharmacology (2020- 3-12) Supplementary table 6: Raw chemical associations to prey proteins ChEMBL25 Supplementary Methods: Computational methods used to propagate tables and supplemental figures Supplementary Discussion: In depth look at the SARS-CoV-2 individual bait subnetworks

deepakunni3 commented 4 years ago

@justaddcoffee If you have your hands full, I can work on this next

justaddcoffee commented 4 years ago

Sure thanks @deepakunni3

lpalbou commented 4 years ago

Let me know if you want some help as I already converted the file in proper json so easy to transform in any way you want.

https://geneontology-public.s3.amazonaws.com/covid-19_targets.json

deepakunni3 commented 4 years ago

@lpalbou Since you are already half way there, would you like to take a stab at this?

justaddcoffee commented 4 years ago

@lpalbou also let @deepakunni3 or @justaddcoffee know if you want to chat briefly about how ingests work in kg_covid_19 - might save you some effort

cmungall commented 4 years ago

See also #19 we want to have uniprot IDs associated with each viral protein, can get from ftp://ftp.ebi.ac.uk/pub/contrib/goa/uniprot_sars-cov-2.gpi

lpalbou commented 4 years ago

Just sorting out a few things here first but yep, in the ingest I will provide a mapping of virus gene name (SARS-CoV-2 E -> Uniprot)

justaddcoffee commented 4 years ago

Hi @lpalbou - any update on this? I think I started an ingest for this, glad to finish this up if you are swamped right now

lpalbou commented 4 years ago

ETA tomorrow would it be fine ?

On Mon, Apr 6, 2020 at 9:43 AM Justin Reese notifications@github.com wrote:

Hi @lpalbou https://github.com/lpalbou - any update on this? I think I started an ingest for this, glad to finish this up if you are swamped right now

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Knowledge-Graph-Hub/kg-covid-19/issues/31#issuecomment-609907020, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZAMDQPKPGRXNVCAZYNPPTRLIBEFANCNFSM4LSFF2MQ .

-- Laurent-Philippe Albou PhD Bioinformatics University of Southern California Affiliate Lawrence Berkeley National Laboratory

justaddcoffee commented 4 years ago

ETA tomorrow would it be fine ?

Sure! Thanks LP

cmungall commented 4 years ago

https://twitter.com/intact_project/status/1247087922005921792?s=19

Note this is now available with other interactions for related viruses from interact 3

On Mon, Apr 6, 2020, 10:14 Justin Reese notifications@github.com wrote:

ETA tomorrow would it be fine ?

Sure! Thanks LP

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Knowledge-Graph-Hub/kg-covid-19/issues/31#issuecomment-609922133, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOLHZW2QVNTDUQ2J7ULRLIENBANCNFSM4LSFF2MQ .

lpalbou commented 4 years ago

They are now speaking of >1200 interactions, nearly 4x the gordon set.

Is this data reliable ? I could update the covid page at some point to show the ribbon for either dataset.

On Mon, Apr 6, 2020 at 11:35 PM Chris Mungall notifications@github.com wrote:

https://twitter.com/intact_project/status/1247087922005921792?s=19

Note this is now available with other interactions for related viruses from interact 3

On Mon, Apr 6, 2020, 10:14 Justin Reese notifications@github.com wrote:

ETA tomorrow would it be fine ?

Sure! Thanks LP

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/Knowledge-Graph-Hub/kg-covid-19/issues/31#issuecomment-609922133 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAAMMOLHZW2QVNTDUQ2J7ULRLIENBANCNFSM4LSFF2MQ

.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Knowledge-Graph-Hub/kg-covid-19/issues/31#issuecomment-610203089, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZAMDTBCOSSUWBGT4G774DRLLCR3ANCNFSM4LSFF2MQ .

-- Laurent-Philippe Albou PhD Bioinformatics University of Southern California Affiliate Lawrence Berkeley National Laboratory

cmungall commented 4 years ago

It is IntAct and Birgit, so yes it's reliable!

I'll leave it to you decide what and how to ingest. Having a PSI-XML adapter will be more generically useful than an ad-hoc adapter for this one supplemental table. But it sounds like you are mostly there, so maybe just complete it, and we make another ticket for psi-xml/intact?

If you wanted, you could get just the Gordon interactions from the XML. It's file unassigned2316.xml in the ingest. This has 27 interactions. Hmm, this sounds too few?...

bmeldal commented 4 years ago

Morning @cmungall and @lpalbou

Yes, this week we released the first big set of coronavirus data, which includes >1200 interactions across multiple papers and includes 27 interactions from the Gorden et al. preprint. The PMID will be updated in the IntAct release following official release of the paper and its PMID assignment.

There will be more CoV data in our next release so a PSI-XML adaptor would be useful for you. We also go through the painful task of manually extracting data from tables etc during curation so you don't have to do it again!

If, in the future, you find interaction preprints that you want to ingest, please check with us to see if we are already processing it.Best way to contact the team is through the "feedback" button on our homepage as that will generate a ticket.

I'll be on the mid-term call today (although, I guess no time for questions/discussion on that call). Happy to set up a separate call as well. My skype is birgit_cb.

Birgit

justaddcoffee commented 4 years ago

This ticket is obviated by #74 - per convo with Birgit, it'd be more efficient to ingest IntAct data which includes the Gordon et al data