Report all models that use a protein-containing complex as an enabler

[vanaukenk]

In order to QC the GPAD output for complex members and contributes_to standard annotations, we would like curators to be able to review their groups' models that have used 'protein containing complexes' as enablers. This would include GO ids for protein-containing complex terms as well as ComplexPortal ids.

Please include in the report:

1. Model id
2. Group
3. Complex id
4. Complex name/label

This query will only report on models where state = production and that satisfy the GO-CAM causal model criteria where at least three activities are linked by two causal relations.

@cmungall

[cmungall]

I can only query things that come out the API @vanaukenk we really need to get gocam objects for everything...

mongo query: activities.enabled_by.term: { $regex: "^GO:" }' -s '[id,title]

[
  {
    "id": "gomodel:5ce58dde00001215",
    "title": "Mouse-Aatf-antiapoptosis"
  },
  {
    "id": "gomodel:5fb9cc0600000156",
    "title": "circadian rhythm and hematopoiesis via ezh2, per1b, cry1a etc. (D. rerio)"
  },
  {
    "id": "gomodel:5fb9cc0600000727",
    "title": "Triacyl lipopetide activation of TLR1-TLR2 complex (Human)"
  },
  {
    "id": "gomodel:5fce9b7300000030",
    "title": "Diacyl lipopeptide and bacteriocin activation of TLR6_TLR2 receptor (Human)\n"
  },
  {
    "id": "gomodel:60418ffa00001019",
    "title": "NLRP3 inflammasome in pyroptosis via nlrp3, caspa, caspb etc. (D. rerio)"
  },
  {
    "id": "gomodel:60e7989d00000165",
    "title": "dTMP biosynthetic process1A (Mouse)"
  },
  {
    "id": "gomodel:61f34dd300000000",
    "title": "Nuclear import of the proteasome by AKIRIN2 (Human)"
  },
  {
    "id": "gomodel:623d156d00000817",
    "title": "Role of TONSL and MMS22L (TONSL-MMS22L complex) in promoting homologous recombination-mediated repair of DSBs (Human)"
  },
  {
    "id": "gomodel:62900b6400001630",
    "title": "PTEN in excitatory hippocampal synapse long-term depression (Human)"
  },
  {
    "id": "gomodel:62900b6400001631",
    "title": "Mycophenolic acid - Penicillium brevicompactum"
  },
  {
    "id": "gomodel:62b4ffe300002959",
    "title": "Aflaroxin (Aspergillus parasiticus)"
  },
  {
    "id": "gomodel:62f58d8800001119",
    "title": "Insulin receptor recycling (Mouse)"
  },
  {
    "id": "gomodel:62f58d8800002184",
    "title": "positive regulation of insulin secretion involved in cellular response to glucose stimulus (Mouse)"
  },
  {
    "id": "gomodel:62f58d8800002367",
    "title": "Protein import into peroxisomes  of PTS1-containing proteins by the PEX5 receptor, and recycling of the PEX5 receptor (S.cerevisiae)"
  },
  {
    "id": "gomodel:62f58d8800006739",
    "title": "Negative regulation of insulin secretion 2 (Mouse)"
  },
  {
    "id": "gomodel:62f58d8800007392",
    "title": "Negative regulation of insulin secretion 3 (Mouse)"
  },
  {
    "id": "gomodel:633b013300001469",
    "title": "Pyruvate catabolic process 2 (Mouse)"
  },
  {
    "id": "gomodel:63e5937500001279",
    "title": "Extraction of mRNA from stalled ribosomes by the SKI complex, leading to recruitment of the PELO-HBS1L complex that binds to stalled ribosomes, followed by ribosome dissociation by ABCE1 (Human)"
  },
  {
    "id": "gomodel:646ff70100000391",
    "title": "Canonical mTORC1 signaling (Human)"
  },
  {
    "id": "gomodel:646ff70100000611",
    "title": "Ubiquitination of RagA/RRAGA by RNF152 inhibits the  mTORC1 signaling (Human)"
  },
  {
    "id": "gomodel:646ff70100001312",
    "title": "Inhibition of the canonical mTORC1 signaling by the GATOR1 complex (Human)"
  },
  {
    "id": "gomodel:646ff70100001877",
    "title": "Inhibition of the canonical mTORC1 signaling via ubiquitination and degradation of LAMTOR1 by UBE3A (Human)"
  },
  {
    "id": "gomodel:646ff70100002094",
    "title": "Negative regulation of the canonical mTORC1 signaling via phosphorylation of LAMTOR4 by PKA (Human)"
  },
  {
    "id": "gomodel:646ff70100002557",
    "title": "Negative regulation  of autophagy via phosphorylation of ULK1 by canonical mTORC1 signaling (Human)"
  },
  {
    "id": "gomodel:6482692800000498",
    "title": "Activation of the canonical mTORC1 signaling by GPR155/LYCHOS in response to cholesterol influx (Human)"
  },
  {
    "id": "gomodel:6482692800000701",
    "title": "Activation of the canonical mTORC1 signaling by BMT2/SAMTOR in response to S-adenosyl-L-methionine influx (Human)"
  },
  {
    "id": "gomodel:64e7eefa00000854",
    "title": "Tumor necrosis factor-mediated signaling pathway 1 (Mouse)"
  },
  {
    "id": "gomodel:65039e8700000196",
    "title": "HTATSF1 and TOPBP1 promote RPA-RAD51 exchange in double-strand break repair via homologous recombination (Human)."
  },
  {
    "id": "gomodel:654d809000000112",
    "title": "SQSTM1 is involved in aggrephagy by mediating recruitment of ubiquitinated proteins to autophagosomes (Human)."
  },
  {
    "id": "gomodel:654d809000000802",
    "title": "Model of MiR-4691-3p inhibition of cGAS-STING signaling in the cytosol (Human)"
  },
  {
    "id": "gomodel:65692e7e00000243",
    "title": "Activation of the canonical mTORC1 signaling by PRMT1 in response to S-adenosyl-L-methionine influx (Human)"
  },
  {
    "id": "gomodel:65a1f4f800000855",
    "title": "Initiation of double-strand break repair via homologous recombination by the MRN  complex (MRE11-RAD50-NBN) (Human)."
  },
  {
    "id": "gomodel:65a1f4f800001029",
    "title": "SKP2 mediates 'Lys-63'-linked ubiquitination of NBN, promoting double-strand break repair via homologous recombination (Human)."
  },
  {
    "id": "gomodel:65a1f4f800001246",
    "title": "Lactylation of MRE11 by CREBBP and NBN by KAT5 in response to DNA damage promotes double-strand break repair via homologous recombination (Human)."
  },
  {
    "id": "gomodel:65a1f4f800002560",
    "title": "Ufmylation of MRE11 promotes ATM activation by the MRN  complex (MRE11-RAD50-NBN) (Human)."
  },
  {
    "id": "gomodel:65a1f4f800002665",
    "title": "Sumoylation of MRE11 by PIAS1 promotes retention of the MRN  complex (MRE11-RAD50-NBN) to DNA damage sites (Human)."
  },
  {
    "id": "gomodel:65bc474400000955",
    "title": "Negative regulation of Hippo signaling by STRIPAK complex via STRN4:MAP4K4(Human)."
  },
  {
    "id": "gomodel:65c57c3400000270",
    "title": "Sxl and Unr inhibit translation of msl-2 transcripts in females (D.melanogaster)."
  },
  {
    "id": "gomodel:65c57c3400001478",
    "title": "Negative regulation of Hippo signaling by SLMAP-STRIPAK complex (Human)."
  },
  {
    "id": "gomodel:65f3ae5c00000170",
    "title": "Ufmylation of RPL26 following translation termination promotes 60S ribosomal subunit recycling (Human)."
  },
  {
    "id": "gomodel:65f3ae5c00000257",
    "title": "Ufmylation of RPL26 following ribosome stalling promotes 60S ribosomal subunit recycling (Human)."
  },
  {
    "id": "gomodel:6606056e00000317",
    "title": "UBR4 and UBR5 catalyze branched-linked polyubiquitination of substrates, leading to proteasome-mediated degradation of  substrates (Human)."
  },
  {
    "id": "gomodel:6606056e00002011",
    "title": "CD72 and BCR co-stimulation by sn/RNP self antigen (Human)"
  },
  {
    "id": "gomodel:66187e4700000078",
    "title": "TREM2 activated by SEMA6D:PLXN1A in dendritic cell. (Human)"
  },
  {
    "id": "gomodel:66187e4700000318",
    "title": "The CRL5(ASB11) complex mediates ubiquitination and degradation of BIK in response to endoplasmic reticulum stress (Human)."
  },
  {
    "id": "gomodel:66187e4700001274",
    "title": "N6 -methyladenosine-modified lncRNA ARHGAP5-AS1 stabilises CSDE1 and coordinates oncogenic RNA regulons in hepatocellular carcinoma. PMID:36354136. (Human)"
  },
  {
    "id": "gomodel:66187e4700002284",
    "title": "septation initiation signaling (GO:0031028) "
  },
  {
    "id": "gomodel:663d668500000596",
    "title": "oxidative phosphorylation (GO:0006119)"
  },
  {
    "id": "gomodel:665912ed00002626",
    "title": "nitrogen cycle metabolic process (GO:0071941)"
  },
  {
    "id": "gomodel:6690711d00000331",
    "title": "iron-sulfur cluster assembly (GO:0016226) and iron-sulfur cluster export from the mitochondrion  (GO:0140466)"
  },
  {
    "id": "gomodel:6690711d00001433",
    "title": "Protein O-linked glycosylation 1 (Mouse)"
  },
  {
    "id": "gomodel:6690711d00002607",
    "title": "ANG tRNA ribonuclease activity inhibits translation in response to stress (Human)."
  },
  {
    "id": "gomodel:6690711d00002652",
    "title": "RNH1 inhibits the tRNA ribonuclease activity of ANG in the cytoplasm in absence of stress (Human)."
  },
  {
    "id": "gomodel:66a3e0bb00002104",
    "title": "ITPRIPL1 is a ligand of CD3E that negatively regulates TCR signaling pathway. (Human)"
  },
  {
    "id": "gomodel:66b5638000002701",
    "title": "IL13RA2-mediated alternative IL13 pathway leading to TGFB1 production (Human)"
  },
  {
    "id": "gomodel:66c7d41500000544",
    "title": "CAAX-box protein maturation 1 (Mouse)"
  },
  {
    "id": "gomodel:66c7d41500000616",
    "title": "CAAX-box protein maturation 2 (Mouse)"
  },
  {
    "id": "gomodel:66c7d41500002919",
    "title": "Heparan sulfate proteoglycan biosynthetic process (Dmel)"
  },
  {
    "id": "gomodel:66e382fb00001225",
    "title": "Protein sumoylation (Mouse)"
  },
  {
    "id": "gomodel:66e382fb00001786",
    "title": "Hepcidin induction by BMP2/BMP6 complex signaling (Human)"
  },
  {
    "id": "gomodel:66f5faaa00000763",
    "title": "NSUN4 catalyzes RNA 5-methylcytosine mark on mitochondrial double-stranded RNAs, which are recognized by C1QBP, promoting RNA degradation by the mitochondrial degradosome complex (Human).\n"
  },
  {
    "id": "gomodel:66f5faaa00001170",
    "title": "RVFV NSs-FBXO3 E3 ligase mediates TFIIH complex degradation. (Human)"
  },
  {
    "id": "gomodel:66f5faaa00001204",
    "title": "Retinoid Metabolic Process 1 (Mouse) "
  },
  {
    "id": "gomodel:67086be200000314",
    "title": "oxidative phosphorylation  (Dmel, somatic)"
  },
  {
    "id": "gomodel:67086be200000519",
    "title": "mitochondrial translation (GO:0032543)"
  },
  {
    "id": "gomodel:67086be200002266",
    "title": "sphingolipid biosynthetic process (GO:0030148)"
  },
  {
    "id": "gomodel:67086be200002592",
    "title": "Retinoid Metabolic Process 3 (Mouse) "
  },
  {
    "id": "gomodel:67086be200002705",
    "title": "Retinoid Metabolic Process 4 (Mouse) "
  },
  {
    "id": "gomodel:671ae02600003194",
    "title": "Negative regulation of cytokine production involved in inflammatory response via calcium influx by CHRNA7 homopentameric and PKC signaling in macrophages (Human)."
  },
  {
    "id": "gomodel:67369e7600000120",
    "title": "mitotic sister chromatid cohesion (GO:0007064)"
  },
  {
    "id": "gomodel:67369e7600006071",
    "title": "Ubiquinone biosynthetic process 1 (Mouse)"
  },
  {
    "id": "gomodel:675b862c00000923",
    "title": "Carnitine shuttle 1 (Mouse)"
  },
  {
    "id": "gomodel:678073a900001673",
    "title": "Inhibin A-mediated suppression of activin A signaling pathway (Human)"
  },
  {
    "id": "gomodel:678073a900002931",
    "title": "fatty acid biosynthetic process (GO:0006633)"
  },
  {
    "id": "gomodel:6796b94c00000168",
    "title": "transcription elongation by RNA polymerase II (GO:0006368) (incomplete)"
  },
  {
    "id": "gomodel:6796b94c00000657",
    "title": "iron-sulfur cluster assembly (Dmel) "
  },
  {
    "id": "gomodel:6796b94c00002252",
    "title": "Transcription-pause release by the PNUTS-PP1 complex (Human)."
  },
  {
    "id": "gomodel:6796b94c00004884",
    "title": "Mo-molybdopterin cofactor biosynthetic process (Dmel)"
  },
  {
    "id": "gomodel:6796b94c00006848",
    "title": "TORC1 signaling (GO:0038202)"
  },
  {
    "id": "gomodel:67b1629100003158",
    "title": "RAB39A and RAB2A-induced HOPS-mediated autophagosome-lysosome fusion (Human)"
  },
  {
    "id": "gomodel:67b1629100003856",
    "title": "ARMC5 mediates RNA polymerase II transcription initiation surveillance by mediating ubiquitination and degradation of POLR2A (Human)."
  },
  {
    "id": "gomodel:67b1629100004023",
    "title": "The INTAC complex mediates RNA polymerase II transcription initiation surveillance by catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit POLR2A and degrading the exiting nascent RNA transcript (Human)."
  },
  {
    "id": "gomodel:YeastPathways_TCA-EUK-PWY",
    "title": "TCA cycle, aerobic respiration - imported from: Saccharomyces Genome Database"
  }
]

[vanaukenk]

Thanks for the query @cmungall

I can only query things that come out the API @vanaukenk we really need to get gocam objects for everything...

Is this just dependent on the upstream work?

[vanaukenk]

@cmungall - is it possible to get the additional info, e.g. group, in the report?
Many of these are obvious, but not all.
Thanks.