- OBO ontology file (MPheno_OBO.ontology.txt in main)
- Contains list of GO terms and details like ID, name, and parents
- Can include different properties than example, like is_obsolete or synonyms
- Required properties: id, name, is_a
- Example format:
[Term]
id: MP:0000015
name: abnormal ear pigmentation
def: "anomaly in the coloration of the skin of the outer ear due to changes in the amount, shape, or distribution of cells producing pigment" [MGI:cwg, MGI:llw2]
is_a: MP:0002095 ! abnormal skin pigmentation
is_a: MP:0030530 ! abnormal outer ear skin morphology
- MGI_Gene_Pheno rpt file (MGI_GenePheno.rpt.txt in main)
- Each line contains MGI ID and one lowest-level MP ID MGI ID is associated with
- Script reads column 5 (MP ID) and column 7 (MGI ID)
- More details about format can be found on MGI site under Alleles and Phenotypes heading (number 9)
- Example format:
Rb1<tm1Tyj>/Rb1<tm1Tyj> Rb1<tm1Tyj> MGI:1857242 involves: 129S2/SvPas MP:0000600 12529408 MGI:97874 MGI:2166359
- MGI_phenotype_ontology file (MGI_phenotype_ontology_data.txt in main)
- Relates gene name, MGI ID, and list of highest-level MP IDs associated with gene (comma-delimited)
- More details about format can be found on MGI site under Alleles and Phenotypes heading (number 2)
- Example format:
Human_Marker_Symbol Human_Entrez_Gene_ID Mouse_Marker_Symbol MGI_Marker_Accession_ID High-level_Mammalian_Phenotype_ID empty_col
A2ML1 144568 Mug1 MGI:99837 MP:0005370, MP:0005376, MP:0005384, MP:0005387, MP:0010768
- Path file (overlapping_paths\all_orthomam_alignment_paths.txt in main)
- File containing all paths to be considered for inclusion in final output path file
- Path should contain _GeneName_ before file extension