kmartinez834
commented
7 months ago @rykahsay instructions are complete now
Closed kmartinez834 closed 3 months ago
kmartinez834
commented
7 months ago @rykahsay instructions are complete now
rykahsay
commented
7 months ago @kmartinez834 ... why do we need to ignore rows if abudance="NA"? Aren't rows missing abundance info good enough?
rykahsay
commented
7 months ago Please check the dataset
kmartinez834
commented
7 months ago Ok to keep rows with abundance ="NA" Checking dataset now
kmartinez834
commented
7 months ago Are "src_xref_key","src_xref_id" required? And would it be more efficient to just have one row with xref_key and src_xref_key rather than two rows for each entry? "xref_key","xref_id","src_xref_key","src_xref_id" "protein_xref_pubmed","37074911","protein_xref_pdc","PDC000471" ~"protein_xref_pdc","PDC000471","protein_xref_pdc","PDC000471"~
For the API, does it matter if "start_aa","end_aa" = "N" or "Asn" ?
rykahsay
commented
6 months ago That is done, here a more important issue: the abundance values are give at "biospecimen_id" level, and multiple values exist for a givem biospecimen_id. On the other hand, our glycan data model is designed to give abundance at the tissue level. This means, if this data is to fit into our existing glycan data model, we need to summarize the abundance levels to the tissue level (for example, we can take the average) -- we need to discuss this in the general meeting.
"uniprotkb_canonical_ac","glycosylation_site_uniprotkb","saccharide","source_tissue_id","source_tissue_name","biospecimen_id","abundance"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000640003","13.28779152"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000640003","14.72918133"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000640003","16.01965604"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000660001","12.09132859"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000660001","14.15798596"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000660001","16.13148149"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000780007","13.7580814"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000780007","14.71911482"
"P02751-15","542","G27058EU","UBERON:0002113","kidney","CPT0000780007","15.94426322"Documenting the discussion we had last week here: Other publication pages include multiple rows for expression (see ex below). We will see if this causes problems when the publication object is created.
https://glygen.org/publication/DOI/10.1016/j.talanta.2020.121495#Expression
kmartinez834
commented
5 months ago Missing page for https://glygen.org/publication/PubMed/37074911
rykahsay
commented
5 months ago check now
kmartinez834
commented
5 months ago Publication page is missing Glycosylation and Expression sections (from human_proteoform_glycosylation_sites_pdc_ccrc.csv)
rykahsay
commented
5 months ago check now:
kmartinez834
commented
5 months ago Issue with pagination, not sure if this is front end or back end... When I click on any other page, it gives no results:
ReneRanzinger
commented
5 months ago @sujeetvkulkarni can you check if the pagination information you send to server are correct for this publication page?
rykahsay
commented
4 months ago @sujeetvkulkarni ... can you please give me the query you are sending. The following queries are working:
$ http POST :4042/publication/detail/ < tests/examples/publication/publication_detail.page.1.json
$ http POST :4042/publication/detail/ < tests/examples/publication/publication_detail.page.2.json Containts of query files:
$ cat tests/examples/publication/publication_detail.page.1.json
{
"id":"30379171",
"type":"PubMed",
"paginated_tables":[
{"table_id":"glycosylation_reported_with_glycan","offset":1,"limit":20,"sort":"start_pos","order":"asc"}
]
}
$ cat tests/examples/publication/publication_detail.page.2.json
{
"id":"30379171",
"type":"PubMed",
"paginated_tables":[
{"table_id":"glycosylation_reported_with_glycan","offset":2,"limit":20,"sort":"start_pos","order":"asc"}
]
}
sujeetvkulkarni
commented
3 months ago Sample query: @rykahsay We use pagination API for server side paginated table. API: https://api.glygen.org/pagination/page/ and below is the payload.
{
"record_type": "publication",
"table_id": "glycosylation_reported_with_glycan",
"record_id": "37074911",
"offset": 21,
"limit": 20,
"order": "asc",
"sort": "start_pos"
}response
{
"query": {
"record_type": "publication",
"table_id": "glycosylation_reported_with_glycan",
"record_id": "37074911",
"offset": 21,
"limit": 20,
"order": "asc",
"sort": "start_pos"
},
"results": []
}results should not be empty array.
rykahsay
commented
3 months ago Please check now:
$ cat tests/temp/q.json
{
"record_type": "publication",
"table_id": "glycosylation_reported_with_glycan",
"record_id": "37074911",
"offset": 21,
"limit": 20,
"order": "asc",
"sort": "start_pos"
}
$ http POST :4442/pagination/page/ < tests/temp/q.json
HTTP/1.1 200 OK
Connection: close
Content-Length: 10827
Content-Type: application/json
Date: Thu, 29 Aug 2024 18:10:52 GMT
Server: gunicorn
{
"query": {
"limit": 20,
"offset": 21,
"order": "asc",
"record_id": "37074911",
"record_type": "publication",
"sort": "start_pos",
"table_id": "glycosylation_reported_with_glycan"
},
"results": [
{
"comment": "",
"end_aa": "N",
"end_pos": 4,
"evidence": [
{
"database": "PubMed",
"id": "37074911",
"url": "https://pubmed.ncbi.nlm.nih.gov/37074911"
},
{
"database": "PDC",
"id": "PDC000471",
"url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471"
}
],
"glytoucan_ac": "G12341GU",
"relation": "attached",
"residue": "Asn",
"site_category": "reported_with_glycan",
"site_lbl": "Asn4",
"site_seq": "MDPnCSCAAGDSCTCAGSCK",
"start_aa": "N",
"start_pos": 4,
"subtype": "",
"type": "N-linked",
@rykahsay as total result count is 40463 so I think pagination is bit slow but its working.
sujeetvkulkarni
commented
3 months ago Adding example label for publication id with large glycosylation table (40463 count) : 37074911.
Source file: downloads/pdc/current/ccRCC_TMT_intact_glycopeptide_abundance_MD-MAD.tsv
Mapping files: unreviewed/human_protein_masterlist.csv generated/misc/pdc_glytoucan_mapping.csv unreviewed/*_protein_glycosylation_motifs.csv misc/n_sequon_info.csv
Output files: human_proteoform_glycosylation_sites_pdc_ccrc.csv
The output file should have the following headers:
if N then "amino_acid" = Asp
If "xref_key" is "protein_xref_pdc" then "xref_id" = "PDC000471"
Example:
Input file
Output file
@ubhuiyan