nataled
commented
9 months ago - [x] For obsolete entries, we sometimes indicate in the OBO stanza some replacement or potential replacement using "replaced_by:" or "consider:", respectively. That information was provided in the table output in the previous incarnation of the website but is missing from the new one. See https://proconsortium.org/app/entry/PR:000053291/ and https://proconsortium.org/app/entry/PR:000047903/ for examples.
- [x] Need better parsing of comment lines. The part "Category=
" goes to the PRO Category section. Specifically, everything between the 'Category=' and the '.' (period) should appear in the PRO Category section. Everything else should appear in a separate section called 'Comment', and that 'Comment' section should appear directly above the PRO Category section. Note the parsing issue for PR:000028342. - [x] The Protein Forms table needs to have each element in a separate column: 'Category', 'Name,' 'Short Label', 'Definition & Comment', 'Comp.', 'Anno.' For the 'Definition & Comment' column, put the definition and comment on separate lines within the cell. Also, the information in the Comp and Anno columns appear to be swapped (that is, currently, if there's annotation then a 'Yes' is appearing in the Comp. column instead of Anno. Simplest fix is to just swap the headers (so Anno comes before Comp). Example term: PR:P35222.
- [x] The Functional Annotation table is missing some information, Part 1. In the first column, please include the proteoform information so that each cell contains (on separate lines): the PRO ID, the short label, and the proteoform information. The proteoform information is found in the definition within the sentence that begins either with 'UniProtKB:' or 'Example'. Use the whole sentence. Example term: PR:P35222.
- [x] The Functional Annotation table is missing some information, Part 2. Looking at the PRO-centric view, the second column under the GO Annotation header contains things like 'increased
". Sometimes the PAF file indicates what the increase (or decrease) is relative to. This information is found in the 8th column of the PAF file, and should be added to the end of the current information. For example, looking at the annotation table for term PR:P35222, the first entry in the annotation table is PR:000030192. This has a GO annotation that has 'enables' and 'increased GO:0003713 transcription coactivator activity'. That second part should read 'increased GO:0003713 transcription coactivator activity relative to PR:000002862 CTNNB1/iso:1/UnMod'. - [x] Additional rows in top table needed. Between 'Parent' and 'Terms by PRO Category' there should be two additional rows: (1) 'Gene Template' and (2) 'Taxon'. Compare https://proconsortium.org/app/entry/PR:P48771/ with https://proconsortium.org/cgi-bin/entry_pro?id=PR:P48771. The Gene Template information should include the identifier and the gene name (each of these can by found on the 'has_gene_template' line of the stanza, like 'has_gene_template
! '. The taxon information use the same arrangement as has_gene_template, except the line will have 'in_taxon' in the stanza (in your code, look for 'in_taxon' instead of 'only_in_taxon' because the substring will find the relevant information already, and at some point in the future all cases of 'only_in_taxon' will be changed to 'in_taxon').