IHMCIF
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Expand ihm_cross_link_list table
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.