Expand ihm_cross_link_list table

[aozalevsky]

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.

[aozalevsky]

Current output:

{
      "match_ids": [
        "SII_7099_1",
        "SII_2602_1",
        "SII_31869_1",
        "SII_20477_1",
        "SII_4874_1"
      ],
      "files": [
        "Bacillus_RNAP-Delta-HelD-S2_PlusSEC_PlusCopurified_SDA_Xi1.7.4_5LinkFDRBB.mzid",
        "Bacillus_RNAP-Delta-HelD-S2_PlusSEC_PlusCopurified_SDA_Xi1.7.4_5LinkFDRBB.mzid",
        "Bacillus_RNAP-Delta-HelD-S2_PlusSEC_PlusCopurified_SDA_Xi1.7.4_5LinkFDRBB.mzid",
        "Bacillus_RNAP-Delta-HelD-S2_PlusSEC_PlusCopurified_SDA_Xi1.7.4_5LinkFDRBB.mzid",
        "Bacillus_RNAP-Delta-HelD-S2_PlusSEC_PlusCopurified_SDA_Xi1.7.4_5LinkFDRBB.mzid"
      ],
      "prot1": "dbseq_HelD_target",
      "prot1_acc": "HelD",
      "pos1": 32,
      "prot2": "dbseq_HelD_target",
      "prot2_acc": "HelD",
      "pos2": 38,
      "crosslinker_accession": "MS:1001460"
    },

[brindakv]

Notes:

• A single PRIDE entry can have multiple mzIdentML files
• evindence_file and evidence_id are terms that are populated in mzIdentML files
• There can be multiple evidence_ids and evidence_files per residue pair
  • For a given Res1 - Res2 pair from the cross link list table, provenance information can be
    • File 1 - ID 1
    • File 1 - ID 2
    • File 2 - ID 1
    • File 2 - ID 2
  • In addition, the same File-ID pair can support multiple residue pairs in the cross link list table
• Create a new table (e.g., ihm_cross_link_list_pxd_provenance) with a composite primary key: cross link list id, pride evidence file, pride evidence id
  • Note: Adding dataset list id or related database accession code here might be helpful although it leads to duplication and can lead to conflicts and errors

[colin-combe]

i realise that the way I've created these "match_ids" is going to cause confusion.

What I've given as a "match_id" is the id of the SpectrumIdentificationItem for the first of the two crosslinked peptides. The other peptide will be within the same SpectrumIdentificationResult.

But the way I've done this is confusing / a bit silly. I think I see this in @brindakv's reply above, which I think assumes there's a different id for the identification of each of the two peptides.

It might be a good idea to change this and include the id for both peptide identifications. Then we could also check that those two SpectrumIdentificationsItems are actually crosslinked to each other. (I leave open the exact formatting of how we include both id's in the data.)

As an aside, I feel like the checking of these things (i.e. retreiving specific id's from mzIdentML file) will be better done with pyteomics than with our reader library. Our reader library is maybe not so useful in this context.

[aozalevsky]

Restraint - > Crosslink_list -> Provenance

New table structure:

Reisude_pair_ID 1 - File_1_ID - SpectrumIdentificationItemID_1 - SpectrumIdentificationItemID_2
Reisude_pair_ID 1 - File_2_ID - SpectrumIdentificationItemID_1- SpectrumIdentificationItemID_2
<...>
Reisude_pair_ID 1 - File_N_ID - SpectrumIdentificationItemID_1_ID - SpectrumIdentificationItemID_2_ID