From cbe4fe7b12f7ab3bd115245b1e24b74b73144c76 Mon Sep 17 00:00:00 2001 From: prashanti Date: Mon, 3 Aug 2015 05:27:48 -0500 Subject: [PATCH] added READMEs --- data/Annotations/README.txt | 32 +++++++++++++++++++++++++++++ data/GeneOrthologs/README.txt | 31 ++++++++++++++++++++++++++++ data/Ontologies/README.txt | 35 ++++++++++++++++++++++++++++++++ results/README.txt | 38 +++++++++++++++++++++++++++++++++++ results/random/README.txt | 38 +++++++++++++++++++++++++++++++++++ 5 files changed, 174 insertions(+) create mode 100644 data/Annotations/README.txt create mode 100644 data/GeneOrthologs/README.txt create mode 100644 data/Ontologies/README.txt create mode 100644 results/README.txt create mode 100644 results/random/README.txt diff --git a/data/Annotations/README.txt b/data/Annotations/README.txt new file mode 100644 index 0000000..dd29628 --- /dev/null +++ b/data/Annotations/README.txt @@ -0,0 +1,32 @@ +Dr-gene-to-phenotype-BF.txt + + This file contains phenotype annotations for zebrafish genes obtained from the Monarch Initiative v1.0. + + Format: tab separated file (.tsv) + + Columns: + 'GeneID': identifier of the gene + 'Annotation': phenotype annotation + +Hs-gene-to-phenotype.txt + + This file contains phenotype annotations for human genes obtained from the Monarch Initiative v1.0. + + Format: tab separated file (.tsv) + + Columns: + 'GeneID': identifier of the gene + 'Annotation': phenotype annotation + +Mm-gene-to-phenotype-BF.txt + + This file contains phenotype annotations for mouse genes obtained from the Monarch Initiative v1.0. + + Format: tab separated file (.tsv) + + Columns: + 'GeneID': identifier of the gene + 'Annotation': phenotype annotation + + + diff --git a/data/GeneOrthologs/README.txt b/data/GeneOrthologs/README.txt new file mode 100644 index 0000000..23cb1c9 --- /dev/null +++ b/data/GeneOrthologs/README.txt @@ -0,0 +1,31 @@ +Human_MGI_orthologs.tsv + + This file contains orthologous pairs of human and mouse genes parsed from PANTHER v9.0. + + Format: tab separated file (.tsv) + + Columns: + 'Mouse gene': identifier of mouse gene + 'Human gene': identifier of orthologous human gene + + +Human_ZFIN_orthologs.tsv + + This file contains orthologous pairs of human and zebrafish genes parsed from PANTHER v9.0. + + Format: tab separated file (.tsv) + + Columns: + 'Zebrafish gene': identifier of mouse gene + 'Human gene': identifier of orthologous human gene + +MGI_ZFIN_orthologs.tsv + + This file contains orthologous pairs of mouse and zebrafish genes parsed from PANTHER v9.0. + + Format: tab separated file (.tsv) + + Columns: + 'Mouse gene': identifier of mouse gene + 'Zebrafish gene': identifier of orthologous zebrafish gene + diff --git a/data/Ontologies/README.txt b/data/Ontologies/README.txt new file mode 100644 index 0000000..b210b3b --- /dev/null +++ b/data/Ontologies/README.txt @@ -0,0 +1,35 @@ +Ontology_R.zip + + This zip file contains ontology R. Ontology R includes MP, ZP, HPO, PATO, UBERON ontologies, equivalence axioms (as of July 9 2015), and grouping classes. + + Format: OWL (Ontology Web Language, ".owl") + + +Ontology_H.zip + + This zip file contains ontology H. Ontology H includes MP, ZP, HPO, PATO, UBERON ontologies, equivalence axioms, homology axioms (as of July 9 2015), and homology grouping classes. + + Format: OWL (Ontology Web Language, ".owl") + + +Ontology_H_random.zip + + This zip file contains ontology H'. Ontology H includes MP, ZP, HPO, PATO, UBERON ontologies, equivalence axioms, homology axioms (as of July 9 2015), and grouping classes. + + Format: OWL (Ontology Web Language, ".owl") + +homology.owl + + This file contains the 1,836 homology axioms obtained from Bgee v0.2. + + Format: (Ontology Web Language, ".owl") + +homology-random.owl + + This file contains the 1,836 randomized homology axioms. + + Format: (Ontology Web Language, ".owl") + +Inquiries: Prashanti Manda, http://orcid.org/0000-0002-7162-7770 + + diff --git a/results/README.txt b/results/README.txt new file mode 100644 index 0000000..7836351 --- /dev/null +++ b/results/README.txt @@ -0,0 +1,38 @@ +Mouse_Human_SimilarityScores.tsv + + This file contains similarity scores for mouse and human orthologous genes computed using ontologies R and H. For format see below. + +Zebrafish_Human_SimilarityScores.tsv + + This file contains similarity scores for zebrafish and human orthologous genes computed using ontologies R and H. For format see below. + +Zebrafish_Mouse_SimilarityScores.tsv + + This file contains similarity scores for mouse and zebrafish orthologous genes computed using ontologies R and H. For format see below. + +Nonorthologs_Mouse_Human_SimilarityScores.tsv + + This file contains similarity scores for mouse and human non-orthologous genes computed using ontologies R and H. For format see below. + +Nonorthologs_Zebrafish_Human_SimilarityScores.tsv + + This file contains similarity scores for zebrafish and human non-orthologous genes computed using ontologies R and H. For format see below. + +Nonorthologs_Zebrafish_Mouse_SimilarityScores.tsv + + This file contains similarity scores for mouse and zebrafish non-orthologous genes computed using ontologies R and H. For format see below. + +Format: tab separated file (.tsv) + +Columns: + 'Gene1': Identifier of first gene in gene pair being compared + 'Gene2': Identifier of second gene in gene pair being compared + 'All Pairs MedianIC With Homology': AP IC of gene pair computed using ontology H + 'All Pairs MedianIC Without Homology': AP IC of gene pair computed using ontology R + 'All Pairs MedianSimJ With Homology': AP SimJ of gene pair computed using ontology H + 'All Pairs MedianSimJ Without Homology': AP SimJ of gene pair computed using ontology R + 'Best Pairs MedianIC With Homology': BP IC of gene pair computed using ontology H + 'Best Pairs MedianIC Without Homology': BP IC of gene pair computed using ontology R + 'Best Pairs MedianSimJ With Homology': BP SimJ of gene pair computed using ontology H + 'Best Pairs MedianSimJ Without Homology': BP IC of gene pair computed using ontology R + diff --git a/results/random/README.txt b/results/random/README.txt new file mode 100644 index 0000000..9863827 --- /dev/null +++ b/results/random/README.txt @@ -0,0 +1,38 @@ +Mouse_Human_SimilarityScores.tsv + + This file contains similarity scores for mouse and human orthologous genes computed using ontologies R and H'. For format see below. + +Zebrafish_Human_SimilarityScores.tsv + + This file contains similarity scores for zebrafish and human orthologous genes computed using ontologies R and H'. For format see below. + +Zebrafish_Mouse_SimilarityScores.tsv + + This file contains similarity scores for mouse and zebrafish orthologous genes computed using ontologies R and H'. For format see below. + +Nonorthologs_Mouse_Human_SimilarityScores.tsv + + This file contains similarity scores for mouse and human non-orthologous genes computed using ontologies R and H'. For format see below. + +Nonorthologs_Zebrafish_Human_SimilarityScores.tsv + + This file contains similarity scores for zebrafish and human non-orthologous genes computed using ontologies R and H'. For format see below. + +Nonorthologs_Zebrafish_Mouse_SimilarityScores.tsv + + This file contains similarity scores for mouse and zebrafish non-orthologous genes computed using ontologies R and H'. For format see below. + +Format: tab separated file (.tsv) + +Columns: + 'Gene1': Identifier of first gene in gene pair being compared + 'Gene2': Identifier of second gene in gene pair being compared + 'All Pairs MedianIC With Homology': AP IC of gene pair computed using ontology H' + 'All Pairs MedianIC Without Homology': AP IC of gene pair computed using ontology R + 'All Pairs MedianSimJ With Homology': AP SimJ of gene pair computed using ontology H' + 'All Pairs MedianSimJ Without Homology': AP SimJ of gene pair computed using ontology R + 'Best Pairs MedianIC With Homology': BP IC of gene pair computed using ontology H' + 'Best Pairs MedianIC Without Homology': BP IC of gene pair computed using ontology R + 'Best Pairs MedianSimJ With Homology': BP SimJ of gene pair computed using ontology H' + 'Best Pairs MedianSimJ Without Homology': BP IC of gene pair computed using ontology R +