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Expand ihm_cross_link_list table #103

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aozalevsky opened this issue Mar 12, 2024 · 0 comments
Open

Expand ihm_cross_link_list table #103

aozalevsky opened this issue Mar 12, 2024 · 0 comments

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@aozalevsky
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To improve the integration with raw crosslinking-MS data Andrea proposed adding an evidence or provenance column to the _ihm_cross_link_list table.

Here is an example of the current API response:

{
  'id': 'SII_139324_1', 
  'file': 'membrane_5pc_1200IDs.mzid', 
  'pass': True, 
  'prot1': 'dbseq_P0A6U8_target', 
  'pos1': 13, 
  'prot2': 'dbseq_P0A6U8_target', 
  'pos2': 46
}

It contains:
file name of the file; one PRIDE entry can contain multiple mzIdentML files
id ID of a specific residue pair in one mzIdentML file. If there are multiple files IDs might overlap.

Since we already have _ihm_cross_link_list.dataset_list_id which points (best case) to PRIDE accession code, we can further expand it to include evindence_file and evidence_id. I suggest we keep file and id to be consistent with PRIDE, but evidence can be replaced with something more suitable.

Both columns can be populated by the depositor, but the more realistic scenario is that it will be done automatically during the deposition.

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