package
0.0.0-20220611144015-40008dcd7b35
Repository: https://github.com/knightjdr/cmgo.git
Documentation: pkg.go.dev
# README
Module name: assessment-localization
Report on which localizations are previously known.
| parameters | definition | default |
|---|---|---|
| goAnnotations | GO annotations in .gaf format | |
| goHierarchy | GO hierarchy in .obo format | |
| localization | list of genes with assigned localizations | |
| namespace | GO namespace to use, one of BP, CC, MF | CC |
| outFile | output file name | localization-known.txt |
| outFileSummary | output file name for summary statistics | summary.txt |
Example file formats
annotationsFile
!Documentation about this header can be found here: https://github.com/geneontology/go-site/blob/master/docs/gaf_validation.md
!
UniProtKB A0A024R161 DNAJC25-GNG10 GO:0003924 GO_REF:0000002 IEA InterPro:IPR001770 F Guanine nucleotide-binding protein subunit gamma DNAJC25-GNG10|hCG_1994888 protein taxon:9606 20190112 InterPro
UniProtKB A0A024R161 DNAJC25-GNG10 GO:0007186 GO_REF:0000002 IEA InterPro:IPR001770|InterPro:IPR015898|InterPro:IPR036284 P Guanine nucleotide-binding protein subunit gamma DNAJC25-GNG10|hCG_1994888 protein taxon:9606 20190112 InterPro
UniProtKB Q9BUL8 PDCD10 GO:0000139 GO_REF:0000039 IEA UniProtKB-SubCell:SL-0134 C Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190112 UniProt
UniProtKB Q9BUL8 PDCD10 GO:0001525 GO_REF:0000037 IEA UniProtKB-KW:KW-0037 P Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190112 UniProt
UniProtKB Q9BUL8 PDCD10 GO:0005515 PMID:16189514 IPI UniProtKB:O00506 F Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL8 PDCD10 GO:0005515 PMID:16189514 IPI UniProtKB:Q9Y6E0 F Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL9 RPP25 GO:0001682 Reactome:R-HSA-5696810 TAS P Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20151024 Reactome
UniProtKB Q9BUL9 RPP25 GO:0003723 PMID:22658674 HDA F Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20140203 UniProt
UniProtKB Q9BUL9 RPP25 GO:0005515 PMID:15096576 IPI UniProtKB:O95707 F Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL9 RPP25 GO:0005515 PMID:21044950 IPI UniProtKB:Q9NYB0 F Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL9 RPP25 GO:0005654 GO_REF:0000052 IDA C Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20141106 HPA
goHierarchy
[Term]
id: GO:0005652
name: nuclear lamina
namespace: cellular_component
def: "The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus." [ISBN:0198506732, ISBN:0716731363]
xref: NIF_Subcellular:sao1455996588
xref: Wikipedia:Nuclear_lamina
is_a: GO:0044428 ! nuclear part
relationship: part_of GO:0034399 ! nuclear periphery
[Term]
id: GO:0005654
name: nucleoplasm
namespace: cellular_component
def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_plant
xref: NIF_Subcellular:sao661522542
xref: Wikipedia:Nucleoplasm
is_a: GO:0044428 ! nuclear part
relationship: part_of GO:0031981 ! nuclear lumen
localization
gene term(s) ID(s) precision
AAAS nuclear outer membrane-endoplasmic reticulum membrane network GO:0042175 0.69
AAK1 cytosol GO:0005829 0.67
AAR2 nucleoplasm GO:0005654 0.66
AARS2 mitochondrial matrix GO:0005759 0.78
AASDH nucleoplasm GO:0005654 0.79
AASS mitochondrial matrix GO:0005759 0.76
Output
localization-known.txt: the input file with a boolean indicating if knownsummary.txt: summary statistics
# Functions
Evaluate determines whether localizations are previously known.