Maping reactome number to pubmed ID
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5.1 years ago
Moses ▴ 120

Dear All,

I have some data in form of TSV that'ts organized as: Uniport_accession GO_ID PMID/REACTOME_NUMBER ontology_type

for example:

CP2D7_HUMAN GO:0006805 PMID:15051713 P
CP2D7_HUMAN GO:0042738 PMID:15051713 P
IFT56_HUMAN GO:0006996 Reactome:R-HSA-1852241 P
TM129_HUMAN GO:0000209 PMID:24807418 P
TM129_HUMAN GO:0030433 PMID:24807418 P
TM129_HUMAN GO:0030970 PMID:24807418 P
E2F8_HUMAN GO:0000122 PMID:16179649 P
E2F8_HUMAN GO:0002040 PMID:22903062 P
E2F8_HUMAN GO:0045944 PMID:22903062 P
UBA6_HUMAN GO:0006511 PMID:17889673 P
UBA6_HUMAN GO:0016567 PMID:17889673 P
LAC7_HUMAN GO:0006898 Reactome:R-HSA-2173782 P
LAC7_HUMAN GO:0006956 Reactome:R-HSA-166663 P
LAC7_HUMAN GO:0006958 Reactome:R-HSA-173623 P
LAC7_HUMAN GO:0038095 Reactome:R-HSA-2454202 P
LAC7_HUMAN GO:0038096 Reactome:R-HSA-2029480 P
LAC7_HUMAN GO:0045087 Reactome:R-HSA-168249 P
LAC7_HUMAN GO:0050776 Reactome:R-HSA-198933 P
SHOT1_HUMAN GO:0007411 Reactome:R-HSA-422475 P
SHOT1_HUMAN GO:2001224 PMID:23864681 P

I want to extract the list of authors associated to each pubmed ID. Given the PMID ive figured out a way to do that, but in some cases as you can see from the example above we have Reactome:R-.... instead of PMIDs. I was wondering how to map these reactome numbers to PMIDs so that I can extract the list of authors that way. Or is there a way to map author names to these reactome numbers? Thank you.

pubmed reactome annotation ontology • 1.7k views
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5.1 years ago
Robin Haw ▴ 160

You can use the remote attribute search to query the Reactome database to extract a list of author names who contributed in annotating a certain protein in a certain publication. If you follow these steps you can generate this file, which is attached. Thanks, Robin

  1. Go to http://www.reactome.org/cgi-bin/remoteattsearch2?DB=gk_current
  2. Choose class “ReactionLikeEvent”
  3. From the fields, first choose “DB_ID”, “with any value”
  4. Click on the “+” and choose “species”, “name”, “matching REGEX” and in the window type “sapiens”
  5. This produces a list of released, human RLEs (9584 instances)
  6. Click on the “Check all” box
  7. From the 4th box at the top, pull down to “custom table” -> a new text box appears above the results.
  8. In here you have to type in the attributes you want as a list. So:

stableIdentifier.identifier

literatureReference.pubMedIdentifier

literatureReference.author._displayName

  1. Click the “view selected instances”
  2. File produced as a tsv file. Save it!
  3. Change the file from a tsv to a csv so it can load directly into excel.
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5.1 years ago
natasha.sernova ★ 3.8k

I found some way to search for PMIDs from Reactome, I am not sure this is the easiest one.

I started from Windows.

I went to

http://www.reactome.org/pages/about/reactome/

then inserted there some number from the list you provided:

R-HSA-198933 P

Then I pressed Search and had a new page, where I selected a single pathway (1) on the left,

(I checked the box in front of it).

Then I received a link to the pathway in the middle of the page,

I’ve pressed on it and received the following page:

http://www.reactome.org/content/detail/R-HSA-198933

with

Literature References almost at the bottom.

pubMedId Title Journal Year

16616474 B cell recognition of membrane-bound antigen: an exquisite way of sensing ligands Curr Opin Immunol 2006

16603343 Immune synapses in T-cell activation Curr Opin Immunol 2006

17218381 Reciprocal regulation of human natural killer cells and macrophages associated with distinct immune synapses

Blood 2007

11244041 The immunological synapse Annu Rev Immunol 2001

18425107 Functions of natural killer cells Nat. Immunol. 2008

16132082 Comparative genomics of natural killer cell receptor gene clusters PLoS Genet. 2005

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yeah I have tried this as well but it's not practical I have on the order of hundred thousand of these reactome numbers that need to be mapped. Also Im hoping to get a 1-to-1 mapping between reactome and PMID.

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