Creating modified forms of proteins

• Modified forms of proteins are used in "active forms" for GO annotation (GAF column 17); or for modified forms acting as substrates in GO annotation extensions (GAF column 16)

For example active form of cut12 is phosphorylated....

.....or in "annotation extensions" to describe substrates, modified forms of histone H3 act as substrates for Clr4 methyltransferase (as both a reader and a writer of histone marks)

• Add a comment to your session to remind you where to add the requested term(s), especially if you need to use modified and unmodified forms

• Check whether the modified form you need already exists here: https://lod.proconsortium.org/yasgui.html

or https://lod.proconsortium.org/yasgui.html#query=PREFIX rdf%3A %3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0APREFIX rdfs%3A %3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0APREFIX owl%3A %3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E %0APREFIX PomBase%3A %3Chttp%3A%2F%2Fwww.pombase.org%2Fspombe%2Fresult%2F%3E%0APREFIX has_gene_template%3A %3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fpr%23has_gene_template%3E%0APREFIX oboInOwl%3A %3Chttp%3A%2F%2Fwww.geneontology.org%2Fformats%2FoboInOwl%23%3E%0ASELECT DISTINCT %3FPRO_term %3FLabel%0AFROM %3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fpr%3E%0AWHERE%0A%7B%0A VALUES %3Fgn_id %7B PomBase%3ASPBC28F2.12 %7D%0A %3FPRO_term rdfs%3AsubClassOf%2B %3Fr . %0A %3Fr owl%3AonProperty has_gene_template%3A . %0A %3Fr owl%3AsomeValuesFrom %3Fgn_id . %0A %3FPRO_term rdfs%3Alabel %3F_Label .%0A OPTIONAL %7B%0A %3Fgn_id rdfs%3Alabel %3Fg%0A %7D .%0A bind(str(%3F_Label) as %3FLabel)%0A%7D%0AORDER BY ASC(%3F_PRO_short_label)%0A&endpoint=https%3A%2F%2Fsparql.proconsortium.org%2Fvirtuoso%2Fsparql&requestMethod=POST&tabTitle=Query&headers=%7B%7D&contentTypeConstruct=text%2Fturtle%2C*%2F*&contentTypeSelect=application%2Fsparql-results%2Bjson%2C*%2F*&q%3D0.9&q%3D0.9&outputFormat=table (here you need to edit the ID in the middle of the string to your gene of interest)

or see the link in this ticket https://github.com/PROconsortium/PRoteinOntology/issues/316

• request term from https://github.com/PROconsortium/PRoteinOntology/issues (include systematic ID, UniProt accession, Protein label, PMID, and a description of the modification in your request)

• Once the term is created, svn update pombe-embl

• copy the OBO stanza to pombe-embl/mini-ontologies/pombe_mini_PRO.obo

Example:

[Term]
id: PR:000059626
name: inner kinetochore subunit cnp20 unphosphorylated 1 (Schizosaccharomyces pombe)
def: "An inner kinetochore subunit cnp20 (Schizosaccharomyces pombe) that has not been phosphorylated on residues equivalent to Ser-3, Thr-8, Ser-12, Ser-13, Ser-14, Thr-21, Ser-23, Thr-29, Ser-31, Ser-33, Thr-36, Ser-39, Thr-43, and Thr-45 of the amino acid sequence represented by UniProtKB:Q9HGK9. Example: UniProtKB:Q9HGK9, Ser-3/Thr-8/Ser-12/Ser-13/Ser-14/Thr-21/Ser-23/Thr-29/Ser-31/Ser-33/Thr-36/Ser-39/Thr-43/Thr-45, PR:000026291." [PRO:DAN, PomBase:VW, PMID:34810257]
comment: Category=organism-modification. Requested by=PomBase.
synonym: "Spom-cnp20/UnPhos:1" EXACT PRO-short-label [PRO:DNx]
synonym: "UniProtKB:Q9HGK9, Ser-3/Thr-8/Ser-12/Ser-13/Ser-14/Thr-21/Ser-23/Thr-29/Ser-31/Ser-33/Thr-36/Ser-39/Thr-43/Thr-45, PR:000026291" NARROW PRO-proteoform-std [PRO:DAN]
property_value: pombase_gene_id SPCC74.03c

No need to include relationship line or intersection_of (logical def):

is_a: PR:000059624 ! inner kinetochore subunit cnp20 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

• Add display name synonym e.g. synonym: "Cnp20/UnPhos-CIM" EXACT PomBase_display_name [PomBase:curators]

The label should be as succinct label possible. This example assessed all P sites in the CIM domain/

• Parent needs a stanza [relation] ID: ! name Minimally: is_a: PR:000000001 ! protein

• svn check-in

• GO back to the Canto session and add the ID for the modified form