Thursday April 16th, 2015: Difference between revisions
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== B. Update from IT group- Data Store, AmiGO2, Justin Elser:== | == B. Update from IT group- Data Store, AmiGO2, Justin Elser:== | ||
===AmiGO2 install=== | |||
AmiGO2 has been installed and loaded with our OWL files, includes some others that may not be needed. Also have around 200,000 annotations loaded from various ontologies. | |||
http://dev.planteome.org | |||
Load times seem much better than the old AmiGO. At least for annotations. Loading the ontologies takes about 25 minutes, but does not include the ncbi taxon ontology. Inclusion of this takes too much memory and doesn't finish on palea. Looking at loading a small subset (plants?) of the taxon. | |||
Test set of annotations loaded: | Test set of annotations loaded: | ||
Revision as of 23:47, 15 April 2015
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Zoom Connection Details: Join from PC, Mac, iOS or Android: https://zoom.us/j/996259332
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A. General Comments and Updates:
B. Update from IT group- Data Store, AmiGO2, Justin Elser:
AmiGO2 install
AmiGO2 has been installed and loaded with our OWL files, includes some others that may not be needed. Also have around 200,000 annotations loaded from various ontologies. http://dev.planteome.org
Load times seem much better than the old AmiGO. At least for annotations. Loading the ontologies takes about 25 minutes, but does not include the ncbi taxon ontology. Inclusion of this takes too much memory and doesn't finish on palea. Looking at loading a small subset (plants?) of the taxon.
Test set of annotations loaded:
- /data/www/planteome_dev/amigo/assoc_files/eo_diversity_arabidopsis.assoc \
- /data/www/planteome_dev/amigo/assoc_files/eo_diversity_rice.assoc \
- /data/www/planteome_dev/amigo/assoc_files/eo_gene.assoc \
- /data/www/planteome_dev/amigo/assoc_files/eo_protein.assoc \
- /data/www/planteome_dev/amigo/assoc_files/eo_qtl.assoc \
- /data/www/planteome_dev/amigo/assoc_files/go_gramene_oryza.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_oryza_gramene.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_oryza_poc.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_vitis_poc.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_zea_MaizeGDB.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_anatomy_qtl_oryza_gramene.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_anatomy_stock_zea_MaizeGDB.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_growth_gene_oryza_gramene.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_growth_gene_vitis_poc.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_growth_qtl_oryza_gramene.assoc \
- /data/www/planteome_dev/amigo/assoc_files/po_ontology_IMP_gene_oryza_poc.assoc \
- /data/www/planteome_dev/amigo/assoc_files/to_diversity_arabidopsis.assoc \
- /data/www/planteome_dev/amigo/assoc_files/to_diversity_rice.assoc \
- /data/www/planteome_dev/amigo/assoc_files/to_Gene_association.assoc \
- /data/www/planteome_dev/amigo/assoc_files/to_Protein_association.assoc \
- /data/www/planteome_dev/amigo/assoc_files/to_QTL_association.assoc