diff --git a/perl_modules/Atlas/ZoomaClient.pm b/perl_modules/Atlas/ZoomaClient.pm index 9c0a40d..539db56 100644 --- a/perl_modules/Atlas/ZoomaClient.pm +++ b/perl_modules/Atlas/ZoomaClient.pm @@ -42,10 +42,13 @@ use URL::Encode qw( url_encode_utf8 ); use JSON::Parse qw( parse_json ); use Array::Compare; use Log::Log4perl; - -use Atlas::Common qw( make_http_request ); +use File::Basename; +use Atlas::Common qw( + make_http_request + get_supporting_file + ); use Atlas::ZoomaClient::MappingResult; - +use HTTP::Request; =head1 ATTRIBUTES @@ -108,6 +111,8 @@ has cutoff_proportion => ( =cut my $logger = Log::Log4perl::get_logger; +my $ontology_lookup = zooma_ontology_lookup(); +my $plant_species = get_plants_species(); =head1 METHODS @@ -122,20 +127,20 @@ more ontology URIs. sub map_term { - my ( $self, $propertyType, $propertyValue ) = @_; + my ( $self, $propertyType, $propertyValue, $organism ) = @_; # Step 1: Get the results from Zooma, an array ref of hash refs # representing the JSON from the Zooma API. - $logger->debug( "Querying zooma for $propertyType : $propertyValue ..." ); + $logger->debug( "Querying zooma for $propertyType : $propertyValue : $organism ..." ); - my $queryResults = $self->_query_zooma( $propertyType, $propertyValue ); + my $queryResults = $self->_query_zooma( $propertyType, $propertyValue, $organism ); unless( $queryResults ) { $logger->warn( "No results found for $propertyType : $propertyValue" ); my $mappingResult = Atlas::ZoomaClient::MappingResult->new( - zooma_error => "No results found for $propertyType : $propertyValue" + zooma_error => "No results found for $propertyType : $propertyValue : $organism" ); return $mappingResult; @@ -150,7 +155,7 @@ sub map_term { # If there are any results, create the mapping result. if( @{ $queryResults } ) { - $logger->debug( "Getting mapping result for $propertyType : $propertyValue ..." ); + $logger->debug( "Getting mapping result for $propertyType : $propertyValue : $organism ..." ); my $mappingResult = Atlas::ZoomaClient::MappingResult->new( zooma_results => $queryResults, @@ -191,22 +196,27 @@ Given a property type and value, return a hash containing the query results. sub _query_zooma { - my ( $self, $propertyType, $propertyValue ) = @_; + my ( $self, $propertyType, $propertyValue, $organism ) = @_; my ( $propertyType4url, $propertyValue4url ) = ( $propertyType, $propertyValue ); # First we need to make sure the property type and value are in the right # format for a URL. $_ = url_encode_utf8( $_ ) for ( $propertyType4url, $propertyValue4url ); + + my $ontology = lc ( get_ontology_for_type( $organism, $propertyType ) ); + $ontology =~ s/\s+$//; # Get the data sources string. my $dataSourcesString = $self->_data_sources_to_string; my $ontologiesString = $self->_ontologies_to_string; + $logger->info("Mapping property type '", $propertyType, "' for species '", $organism, "' with ontology db - ", $ontology); + # Build the query URL. my $queryURL = $self->get_zooma_api_base . "services/annotate?propertyValue=$propertyValue4url&propertyType=$propertyType4url" - . "&filter=required:[$dataSourcesString],preferred:[$dataSourcesString],ontologies:[$ontologiesString]"; + . "&filter=required:[$dataSourcesString],preferred:[$dataSourcesString],ontologies:[$ontology]"; my $zoomaJSON = make_http_request( $queryURL, "json" ); @@ -244,6 +254,71 @@ sub _query_zooma { } +sub zooma_ontology_lookup { + my ( $filename ) = @_; + my $abs_path = dirname(File::Spec->rel2abs(__FILE__)); + my $zoomaOntologyLookupFile = get_supporting_file( 'zooma_ontologies.tsv' ); + open (my $in_fh, '<', $zoomaOntologyLookupFile) or die $!; + my %ontology_lookup; + while ( my $line = <$in_fh> ) { + my ( $property_type, $organism, $ontologies ) = split /\t/, $line; + $ontology_lookup{$property_type}{$organism} = $ontologies; + } + return \%ontology_lookup; +} + +sub get_plants_species { + + # Plants file comes from + # http://ftp.ebi.ac.uk/ensemblgenomes/pub/release-51/plants/species_EnsemblPlants.txt, + # but the Ensembl FTP is a bit unreliable, so we bundle it here. + + my $plants_file=get_supporting_file( 'species_EnsemblPlants.txt' ); + open(PLANTS, $plants_file) or die("Could not open file $plants_file."); + my @plants_species_list; + foreach my $line () { + next if $line =~ m/#name/; + my @plants_species = split(/\t/,$line); + push (@plants_species_list, $plants_species[1]); + } + close(PLANTS); + return \@plants_species_list; +} + + +sub get_ontology_for_type { + my ( $organism, $property_type ) = @_; + + my $ontology; + ## for plants specific + if (grep { $_ =~ $organism } @{ $plant_species }) { + print ("plant species - $organism \n"); + #set organism to plants + my $organism='plants'; + } + ## iterate over the lookup table to identify corresponding ontology db for zooma mappings + foreach my $propertyType ( sort keys %{ $ontology_lookup } ) { + if ( $propertyType =~ $property_type ){ + foreach my $species ( sort keys %{ $ontology_lookup->{$propertyType} } ) { + if ( $species =~ $organism ){ + $ontology = $ontology_lookup->{$propertyType}->{$species}; + } + elsif ( $species =~ 'any' ){ + $ontology = $ontology_lookup->{$propertyType}->{'any'}; + } + elsif ( $species =~ 'other'){ + $ontology = $ontology_lookup->{$propertyType}->{'other'}; + } + } + return $ontology; + } + else { + $ontology='EFO'; + } + } + return $ontology; +} + =item _data_sources_to_string Converts data sources array ref into a comma-separated string and returns it. diff --git a/supporting_files/ArrayExpressSiteConfig.yml.default b/supporting_files/ArrayExpressSiteConfig.yml.default index 860be7c..6c0d770 100755 --- a/supporting_files/ArrayExpressSiteConfig.yml.default +++ b/supporting_files/ArrayExpressSiteConfig.yml.default @@ -2,33 +2,33 @@ # This file contains definitions for variables used throughout ArrayExpress and # Expression Atlas production code. -MX_DSN: DBI:mysql:prod_miamexpress:mysql-prod-miamexpress.ebi.ac.uk:4054 +MX_DSN: xxxx MX_USERNAME: xxxx MX_PASSWORD: xxxx -AE2_INSTANCE_NAME: AE2PRD -AE2_DSN: DBI:Oracle:host=ora-vm5-022.ebi.ac.uk;sid=AE2PRO;port=1531 +AE2_INSTANCE_NAME: xxxx +AE2_DSN: xxxx AE2_USERNAME: xxxx AE2_PASSWORD: xxxx -AEDW_DSN: DBI:Oracle:host=ora-vm-064.ebi.ac.uk;sid=ATLASPRO;port=1531 +AEDW_DSN: xxxx AEDW_USERNAME: xxxx AEDW_PASSWORD: xxxx -AE_PG_DSN: dbi:Pg:dbname=gxpatlaspro;host=pgsql-hxvm-002.ebi.ac.uk;port=5432 +AE_PG_DSN: xxx AE_PG_USERNAME: xxxx AE_PG_PASSWORD: xxxx # Submissions Tracking MySQL back-end -AUTOSUBS_DSN: DBI:mysql:ae_autosubs:mysql-ae-autosubs-prod.ebi.ac.uk:4091 +AUTOSUBS_DSN: xxxx AUTOSUBS_USERNAME: xxxx AUTOSUBS_PASSWORD: xxxx -AUTOSUBMISSIONS_FILEBASE: /nfs/ma/ma-exp/AutoSubmissions/ -AUTOSUBMISSIONS_TARGET: /nfs/ma/home/arrayexpress/ae2_production/data/EXPERIMENT -GEO_SUBMISSIONS_TARGET: /nfs/production3/ma/home/atlas3-production/GEO_import -ENA_SUBMISSIONS_TARGET: /nfs/production3/ma/home/atlas3-production/ENA_import -AUTOSUBMISSIONS_ARRAY_TARGET: /nfs/production3/ma/home/atlas3-production/GEO_import/microarray/ARRAY +AUTOSUBMISSIONS_FILEBASE: +AUTOSUBMISSIONS_TARGET: +EO_SUBMISSIONS_TARGET: +ENA_SUBMISSIONS_TARGET: +AUTOSUBMISSIONS_ARRAY_TARGET: AUTOSUBS_ADMIN: fg_cur@ebi.ac.uk AUTOSUBS_ADMIN_USERNAME: xxxx @@ -41,7 +41,7 @@ AUTOSUBS_ADMIN_USERNAME: xxxx AUTOSUBS_CURATOR_EMAIL: fgsubs@ebi.ac.uk -HTTP_PROXY: 'http://www-proxy.ebi.ac.uk:3128' +HTTP_PROXY: AE_ARRAYDESIGN_LIST: 'http://peach.ebi.ac.uk:8480/api/all-arrays.txt' @@ -49,40 +49,38 @@ MAX_LWP_DOWNLOAD: 10104857600 ENA_FTP_URI: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ -AE2_LOAD_DIR: /nfs/ma/home/arrayexpress/ae2_production/data +AE2_LOAD_DIR: BIOPORTAL_API_KEY: xxxx -ONTO_TERMS_LIST: /nfs/production3/ma/home/atlas3-production/sw/configs/onto_terms.yml +ONTO_TERMS_LIST: # file used to process GEO experiments. -#GEO_IMPORT_COMMAND: 'PERL5LIB=/nfs/ma/home/fgpt/sw/lib/perl/CentOS_prod/lib64/perl5/site_perl:/nfs/ma/home/fgpt/sw/lib/perl/CentOS_prod/lib:/nfs/ma/home/fgpt/sw/lib/perl/FGPT_CentOS_prod/lib /usr/bin/perl /nfs/ma/home/fgpt/sw/lib/perl/FGPT_CentOS_prod/new_soft2magetab.pl' -GEO_IMPORT_COMMAND: '/nfs/production3/ma/home/atlas3-production/sw/atlasinstall_prod/atlasprod/geo_import/new_soft2magetab.pl' +GEO_IMPORT_COMMAND: 'new_soft2magetab.pl' -GEO_STAGING_DIR: /nfs/production3/ma/home/atlas3-production/GEO_import/GEOImportDownload/ +GEO_STAGING_DIR: GEOImportDownload/ -GSE_GDS_MAP: /nfs/production3/ma/home/atlas3-production/GEO_import/geo_import_supporting_files/gse2gds.txt -GEO_PLATFORM_MAP: /nfs/production3/ma/home/atlas3-production/GEO_import/geo_import_supporting_files/platforms.txt +GSE_GDS_MAP: geo_import_supporting_files/gse2gds.txt +GEO_PLATFORM_MAP: geo_import_supporting_files/platforms.txt # New: location of EFO and ontology mapping script for use in GEO import EFO_LOCATION: http://www.ebi.ac.uk/efo/efo.owl -EFO_OWL_FILE: /nfs/production3/ma/home/atlas3-production/GEO_import/geo_import_supporting_files/efo.owl -#OE_MAPPING_SCRIPT: /nfs/ma/ma-subs/AE/subs/PERL_SCRIPTS/local/bin/add_ontology_refs_to_magetab.pl +EFO_OWL_FILE: geo_import_supporting_files/efo.owl -ENA_ACC_MAP: /nfs/production3/ma/home/atlas3-production/GEO_import/geo_import_supporting_files/fastqFileReport +ENA_ACC_MAP: geo_import_supporting_files/fastqFileReport VALIDATION_SCRIPT: # Location of ADF and Experiments checked in Atlas.pm -ADF_CHECKED_LIST: /nfs/production3/ma/home/atlas3-production/sw/configs/adfs_not_in_atlas.txt -ATLAS_EXPT_CHECKED_LIST: /nfs/production3/ma/home/atlas3-production/sw/configs/expts_checked_for_atlas.txt +ADF_CHECKED_LIST: configs/adfs_not_in_atlas.txt +ATLAS_EXPT_CHECKED_LIST: configs/expts_checked_for_atlas.txt SKIP_CHECKED_LIST_FILES: true PRIVATE_ADF_USERNAME: xxxx PRIVATE_ADF_PASSWORD: xxxxx PRIVATE_ADF_URI_BASE: http://www.ebi.ac.uk/arrayexpress/files/ -ADF_DB_PATTERN_FILE: /nfs/production3/ma/home/atlas3-production/sw/configs/adf_db_patterns.txt +ADF_DB_PATTERN_FILE: configs/adf_db_patterns.txt diff --git a/supporting_files/AtlasSiteConfig.yml.default b/supporting_files/AtlasSiteConfig.yml.default index b56671b..1250254 100644 --- a/supporting_files/AtlasSiteConfig.yml.default +++ b/supporting_files/AtlasSiteConfig.yml.default @@ -5,7 +5,7 @@ atlasinstall: prod # annotare import -arrayexpress_experiment_load_dir: /ebi/microarray/home/arrayexpress/ae2_production/data/EXPERIMENT +arrayexpress_experiment_load_dir: # geo import geo_experiment_load_dir: /GEO_import @@ -22,7 +22,7 @@ ena_sc_experiment_load_dir: /singlecell/experiment #File containing factor values to use as references in differential # experiments and factor types to ignore. -references_ignore_file: sw/atlasinstall_prod/atlasprod/analysis/differential/mapped_reference_assay_group_factor_values.xml +references_ignore_file: mapped_reference_assay_group_factor_values.xml # Allowed experiment types in XML configuration file. allowed_xml_experiment_types: @@ -58,7 +58,7 @@ mirna_array_design_accessions: mirbase_mappings_write_directory: arraydesigns/microRNA # URL base for ArrayExpress files. -array_designs_ftp_site: /net/nasP/ftp_public/databases/microarray/data/array +array_designs_ftp_site: # File mapping abbreviations used for species in miRBase. mirbase_species_abbreviations: bioentity_properties/mirbase/idprefix_to_organism.tsv @@ -67,28 +67,25 @@ mirbase_species_abbreviations: bioentity_properties/mirbase/idprefix_to_organism contrast_details_url: http://wwwdev.ebi.ac.uk/gxa/api/contrastdetails.tsv # File containing mappings of property types to EFO URIs. -property_types_efo_mappings: sw/atlasinstall_prod/atlasprod/db/scripts/property_types_efo_mappings.tsv +property_types_efo_mappings: property_types_efo_mappings.tsv # Directory where Ensembl annotation source files live. -annotation_source_dir: sw/atlasinstall_prod/atlasprod/bioentity_annotations/ensembl/annsrcs +annotation_source_dir: annsrcs # Genome references config. -genome_references_config: sw/islinstall_prod/isl_genomes/genome_references.conf +genome_references_config: genome_references.conf # R installation. -atlas_r_installation: sw/atlasinstall_prod/R_install +atlas_r_installation: R_install # Script for querying CTTV EFO terms. -cttv_efo_sparql_script: sw/atlasinstall_prod/atlasprod/db/scripts/get_efo_in_cttv_validation_data.sh - -# File containing property types and values to exclude from Zooma mapping. -zooma_exclusions_file: /atlasprod/supporting_files/zooma_exclusions.yml +cttv_efo_sparql_script: get_efo_in_cttv_validation_data.sh # File containing accessions of experiments that have been assessed by a curator. -atlas_curated_accessions_file: sw/configs/atlas_curated_accessions.yml +atlas_curated_accessions_file: atlas_curated_accessions.yml # File containing accessions of experiments that don't have R experiment summaries. -no_r_data_accessions_file: sw/configs/no_r_object +no_r_data_accessions_file: no_r_object # URL to get ADF info from ArrayExpress. arrayexpress_adf_info_url: http://peach.ebi.ac.uk:8480/api/array.txt?acc= @@ -188,13 +185,11 @@ atlas_supported_adfs: A-GEOD-11534: Rattus norvegicus A-MEXP-1414: Oryza sativa -failed_qc_dir: /nfs/production3/ma/home/atlas3-production/failedQC - -min_pval_dir: /nfs/production3/ma/home/atlas3-production/minPValGt0.5 +failed_qc_dir: failedQC -failed_curation_dir: /nfs/production3/ma/home/atlas3-production/failedCuration +min_pval_dir: atlas3-production/minPValGt0.5 -non_standard_experiments_file: /atlasprod/supporting_files/non_standard_experiments.yml +failed_curation_dir: failedCuration atlasprd3_dsn: DBI:Oracle:host=ora-vm-xxx.ebi.ac.uk;sid=ATLASPRO;port=1531 atlasprd3_user: xxxx diff --git a/supporting_files/species_EnsemblPlants.txt.default b/supporting_files/species_EnsemblPlants.txt.default new file mode 100644 index 0000000..31da2ea --- /dev/null +++ b/supporting_files/species_EnsemblPlants.txt.default @@ -0,0 +1,115 @@ +#name species division taxonomy_id assembly assembly_accession genebuild variation microarray pan_compara peptide_compara genome_alignments other_alignments core_db species_id +Actinidia chinensis actinidia_chinensis EnsemblPlants 1590841 Red5_PS1_1.69.0 GCA_003024255.1 2018-04ENA N N N Y Y N actinidia_chinensis_core_51_104_1 1 +Aegilops tauschii aegilops_tauschii EnsemblPlants 200361 Aet v4.0 GCA_002575655.1 2017-10-UCD N Y N Y Y Y aegilops_tauschii_core_51_104_3 1 +Amborella trichopoda amborella_trichopoda EnsemblPlants 13333 AMTR1.0 GCA_000471905.1 2014-01-AGD N N Y Y Y Y amborella_trichopoda_core_51_104_1 1 +Ananas comosus ananas_comosus EnsemblPlants 4615 F153 GCA_902162155.1 2019-10-UIL N N N Y Y N ananas_comosus_core_51_104_1 1 +Arabidopsis halleri arabidopsis_halleri EnsemblPlants 63677 Ahal2.2 GCA_900078215.1 2016-09-UZH N Y N Y Y Y arabidopsis_halleri_core_51_104_1 1 +Arabidopsis lyrata arabidopsis_lyrata EnsemblPlants 81972 v.1.0 GCA_000004255.1 2008-12-JGI N N N Y Y Y arabidopsis_lyrata_core_51_104_10 1 +Arabidopsis thaliana arabidopsis_thaliana EnsemblPlants 3702 TAIR10 GCA_000001735.1 2016-06-Araport11 Y Y Y Y Y Y arabidopsis_thaliana_core_51_104_11 1 +Arabis alpina arabis_alpina EnsemblPlants 50452 A_alpina_V4 GCA_000733195.1 2014-08-TRANSNET N N N N N N arabis_alpina_core_51_104_1 1 +Asparagus officinalis asparagus_officinalis EnsemblPlants 4686 Aspof.V1 GCA_001876935.1 2019-11-UniversityofGeorgia N N N Y Y N asparagus_officinalis_core_51_104_1 1 +Beta vulgaris beta_vulgaris EnsemblPlants 3555 RefBeet-1.2.2 GCA_000511025.2 2015-07-BOKU N N N Y Y Y beta_vulgaris_core_51_104_2 1 +Brachypodium distachyon brachypodium_distachyon EnsemblPlants 15368 Brachypodium_distachyon_v3.0 GCA_000005505.4 2018-01-JGI Y N Y Y Y Y brachypodium_distachyon_core_51_104_4 1 +Brassica napus brassica_napus EnsemblPlants 3708 AST_PRJEB5043_v1 GCA_000751015.1 2015-09-GSC N Y N Y Y Y brassica_napus_core_51_104_1 1 +Brassica oleracea brassica_oleracea EnsemblPlants 109376 BOL GCA_000695525.1 2014-05-CanSeq N Y N Y Y Y brassica_oleracea_core_51_104_1 1 +Brassica rapa brassica_rapa EnsemblPlants 3711 Brapa_1.0 GCA_000309985.1 2012-03-IVFCAAS N Y N Y Y Y brassica_rapa_core_51_104_1 1 +Camelina sativa camelina_sativa EnsemblPlants 90675 Cs GCA_000633955.1 2020-02-Cs_genes_V2 N N N Y N N camelina_sativa_core_51_104_1 1 +Cannabis sativa female cannabis_sativa_female EnsemblPlants 3483 cs10 GCA_900626175.1 2020-02-CS10 N N N Y Y N cannabis_sativa_female_core_51_104_1 1 +Capsicum annuum capsicum_annuum EnsemblPlants 4072 ASM51225v2 GCA_000512255.2 2017-11-ENA N N N Y Y N capsicum_annuum_core_51_104_2 1 +Chara braunii chara_braunii EnsemblPlants 69332 Cbr_1.0 GCA_003427395.1 2018-10-KanazawaUniversity N N N Y N N chara_braunii_core_51_104_1 1 +Chenopodium quinoa chenopodium_quinoa EnsemblPlants 63459 ASM168347v1 GCA_001683475.1 2020-07-maker N N N Y Y N chenopodium_quinoa_core_51_104_1 1 +Chlamydomonas reinhardtii chlamydomonas_reinhardtii EnsemblPlants 3055 Chlamydomonas_reinhardtii_v5.5 GCA_000002595.3 2018-01-JGI N N Y Y Y Y chlamydomonas_reinhardtii_core_51_104_3 1 +Chondrus crispus chondrus_crispus EnsemblPlants 2769 ASM35022v2 GCA_000350225.2 2015-09-Genoscope N N N Y Y N chondrus_crispus_core_51_104_1 1 +Citrullus lanatus citrullus_lanatus EnsemblPlants 3654 Cla97_v1 GCA_000238415.2 2020-02-Cla97 N N N Y Y N citrullus_lanatus_core_51_104_1 1 +Citrus clementina citrus_clementina EnsemblPlants 85681 Citrus_clementina_v1.0 GCA_000493195.1 2013-11-ENA N N N Y Y N citrus_clementina_core_51_104_1 1 +Coffea canephora coffea_canephora EnsemblPlants 49390 AUK_PRJEB4211_v1 GCA_900059795.1 2015-09-ENA N N N Y Y N coffea_canephora_core_51_104_1 1 +Corchorus capsularis corchorus_capsularis EnsemblPlants 210143 CCACVL1_1.0 GCA_001974805.1 2017-02-BJRI N N N Y Y Y corchorus_capsularis_core_51_104_1 1 +Cucumis melo cucumis_melo EnsemblPlants 3656 Melonv4 GCA_902497455.1 2020-02-melonomics N N N Y Y N cucumis_melo_core_51_104_1 1 +Cucumis sativus cucumis_sativus EnsemblPlants 3659 ASM407v2 GCA_000004075.2 2014-10-BGI N N N Y Y Y cucumis_sativus_core_51_104_2 1 +Cyanidioschyzon merolae cyanidioschyzon_merolae EnsemblPlants 280699 ASM9120v1 GCA_000091205.1 2019-12-NIG N N Y Y Y N cyanidioschyzon_merolae_core_51_104_1 1 +Cynara cardunculus cynara_cardunculus EnsemblPlants 59895 CcrdV1 GCA_001531365.1 2018-04-ENA N N N Y Y N cynara_cardunculus_core_51_104_1 1 +Daucus carota daucus_carota EnsemblPlants 79200 ASM162521v1 GCA_001625215.1 2016-06-USDA N N N Y Y Y daucus_carota_core_51_104_1 1 +Dioscorea rotundata dioscorea_rotundata EnsemblPlants 55577 TDr96_F1_v2_PseudoChromosome GCA_009730915.1 2020-06-v2.0 N N N Y Y N dioscorea_rotundata_core_51_104_3 1 +Eragrostis curvula eragrostis_curvula EnsemblPlants 38414 CERZOS_E.curvula1.0 GCA_007726485.1 2019-09-CERZOSCONICET N N N Y Y N eragrostis_curvula_core_51_104_1 1 +Eragrostis tef eragrostis_tef EnsemblPlants 110835 ASM97063v1 GCA_000970635.1 2019-05-TPI N N N Y Y N eragrostis_tef_core_51_104_1 1 +Eucalyptus grandis eucalyptus_grandis EnsemblPlants 71139 Egrandis1_0 GCA_000612305.1 2017-09-Geneglob N N N Y Y N eucalyptus_grandis_core_51_104_1 1 +Eutrema salsugineum eutrema_salsugineum EnsemblPlants 72664 Eutsalg1_0 GCA_000478725.1 2013-11-JointGenomeInstitute N N N N N Y eutrema_salsugineum_core_51_104_1 1 +Galdieria sulphuraria galdieria_sulphuraria EnsemblPlants 130081 ASM34128v1 GCA_000341285.1 2013-02-GsGP N N N Y Y N galdieria_sulphuraria_core_51_104_1 1 +Glycine max glycine_max EnsemblPlants 3847 Glycine_max_v2.1 GCA_000004515.4 2018-08-JGI N Y N Y Y Y glycine_max_core_51_104_4 1 +Gossypium raimondii gossypium_raimondii EnsemblPlants 29730 Graimondii2_0_v6 GCA_000327365.1 2017-09-DOEJointGenomeInstitute N N N Y Y Y gossypium_raimondii_core_51_104_2 1 +Helianthus annuus helianthus_annuus EnsemblPlants 4232 HanXRQr1.0 GCA_002127325.1 2017-09-ICSG Y N N Y Y Y helianthus_annuus_core_51_104_1 1 +Hordeum vulgare hordeum_vulgare EnsemblPlants 112509 IBSC v2 GCA_901482405.1 2019-04-IBSC Y Y N Y Y Y hordeum_vulgare_core_51_104_3 1 +Hordeum vulgare GoldenPromise hordeum_vulgare_goldenpromise EnsemblPlants 112509 GPv1 GCA_902500625.1 2020-02-TRITEX N N N N N N hordeum_vulgare_goldenpromise_core_51_104_1 1 +Hordeum vulgare TRITEX hordeum_vulgare_tritex EnsemblPlants 112509 Morex_V2_scaf GCA_903813605.1 2020-12-IPK N N N N N N hordeum_vulgare_tritex_core_51_104_1 1 +Ipomoea triloba ipomoea_triloba EnsemblPlants 35885 ASM357664v1 GCA_003576645.1 2019-09-GT4SP N N N Y Y N ipomoea_triloba_core_51_104_1 1 +Juglans regia juglans_regia EnsemblPlants 51240 Walnut_2.0 GCA_001411555.2 2020-11-UCD N N N Y Y N juglans_regia_core_51_104_1 1 +Kalanchoe fedtschenkoi kalanchoe_fedtschenkoi EnsemblPlants 63787 K_fedtschenkoi_M2_v1 GCA_002312845.1 2020-04-v1.0 N N N N N N kalanchoe_fedtschenkoi_core_51_104_1 1 +Leersia perrieri leersia_perrieri EnsemblPlants 77586 Lperr_V1.4 GCA_000325765.3 2013-09-OGE N N N Y Y Y leersia_perrieri_core_51_104_14 1 +Lupinus angustifolius lupinus_angustifolius EnsemblPlants 3871 LupAngTanjil_v1.0 GCA_001865875.1 2017-07-CSIRO N N N Y Y Y lupinus_angustifolius_core_51_104_1 1 +Malus domestica Golden malus_domestica_golden EnsemblPlants 3750 ASM211411v1 GCA_002114115.1 2019-12-GDDH13 Y N N Y Y N malus_domestica_golden_core_51_104_1 1 +Manihot esculenta manihot_esculenta EnsemblPlants 3983 Manihot esculenta v6 GCA_001659605.1 2017-09-JGI N N N Y Y Y manihot_esculenta_core_51_104_1 1 +Marchantia polymorpha marchantia_polymorpha EnsemblPlants 3197 Marchanta_polymorpha_v1 GCA_003032435.1 2018-04-ENA N N Y Y Y N marchantia_polymorpha_core_51_104_1 1 +Medicago truncatula medicago_truncatula EnsemblPlants 3880 MedtrA17_4.0 GCA_000219495.2 2014-06-ENA N Y N Y Y Y medicago_truncatula_core_51_104_2 1 +Musa acuminata musa_acuminata EnsemblPlants 214687 Musa_acuminata_v2 GCA_904845865.1 2016-01-BGH N N N Y Y Y musa_acuminata_core_51_104_2 1 +Nicotiana attenuata nicotiana_attenuata EnsemblPlants 49451 NIATTr2 GCA_001879085.1 2017-09-MPI-CE N Y N Y Y Y nicotiana_attenuata_core_51_104_1 1 +Nymphaea colorata nymphaea_colorata EnsemblPlants 210225 ASM883128v1 GCA_008831285.1 2020-02-asm20170215 N N N Y Y N nymphaea_colorata_core_51_104_1 1 +Olea europaea var. sylvestris olea_europaea_sylvestris EnsemblPlants 158386 O_europaea_v1 GCA_002742605.1 2019-10-ORCAE N N N Y Y N olea_europaea_sylvestris_core_51_104_1 1 +Oryza barthii oryza_barthii EnsemblPlants 65489 O.barthii_v1 GCA_000182155.2 2014-05-OGE N Y N Y Y Y oryza_barthii_core_51_104_3 1 +Oryza brachyantha oryza_brachyantha EnsemblPlants 4533 Oryza_brachyantha.v1.4b GCA_000231095.2 2011-05-OGE N N N Y Y Y oryza_brachyantha_core_51_104_14 1 +Oryza glaberrima oryza_glaberrima EnsemblPlants 4538 Oryza_glaberrima_V1 GCA_000147395.1 2011-05-OGE Y Y N Y Y Y oryza_glaberrima_core_51_104_2 1 +Oryza glumipatula oryza_glumipatula EnsemblPlants 40148 Oryza_glumaepatula_v1.5 GCA_000576495.1 2013-09-OGE Y Y N Y Y Y oryza_glumipatula_core_51_104_15 1 +Oryza sativa Indica Group oryza_indica EnsemblPlants 39946 ASM465v1 GCA_000004655.2 2010-07-BGI Y Y N Y Y Y oryza_indica_core_51_104_2 1 +Oryza longistaminata oryza_longistaminata EnsemblPlants 4528 O_longistaminata_v1.0 GCA_000789195.1 2015-05-OGE N Y N Y Y Y oryza_longistaminata_core_51_104_2 1 +Oryza meridionalis oryza_meridionalis EnsemblPlants 40149 Oryza_meridionalis_v1.3 GCA_000338895.2 2014-10-OGE N Y N Y Y Y oryza_meridionalis_core_51_104_13 1 +Oryza nivara oryza_nivara EnsemblPlants 4536 Oryza_nivara_v1.0 GCA_000576065.1 2013-09-OGE N Y N Y Y Y oryza_nivara_core_51_104_10 1 +Oryza punctata oryza_punctata EnsemblPlants 4537 Oryza_punctata_v1.2 GCA_000573905.1 2013-09-OGE N Y N Y Y Y oryza_punctata_core_51_104_12 1 +Oryza rufipogon oryza_rufipogon EnsemblPlants 4529 OR_W1943 GCA_000817225.1 2013-09-OGE N Y N Y Y Y oryza_rufipogon_core_51_104_11 1 +Oryza sativa Japonica Group oryza_sativa EnsemblPlants 39947 IRGSP-1.0 GCA_001433935.1 2019-06-RAPDB Y Y Y Y Y Y oryza_sativa_core_51_104_7 1 +Ostreococcus lucimarinus ostreococcus_lucimarinus EnsemblPlants 436017 ASM9206v1 GCA_000092065.1 2011-01-JGI N N N N N Y ostreococcus_lucimarinus_core_51_104_1 1 +Panicum hallii HAL2 panicum_hallii EnsemblPlants 1504633 PhalliiHAL_v2.1 GCA_003061485.1 2018-05ENA N N N Y Y N panicum_hallii_core_51_104_1 1 +Panicum hallii FIL2 panicum_hallii_fil2 EnsemblPlants 206008 PHallii_v3.1 GCA_002211085.2 2018-05ENA N N N Y Y N panicum_hallii_fil2_core_51_104_1 1 +Papaver somniferum papaver_somniferum EnsemblPlants 3469 ASM357369v1 GCA_003573695.1 2019-06-XianJiaotongUniversity N N N Y Y N papaver_somniferum_core_51_104_1 1 +Phaseolus vulgaris phaseolus_vulgaris EnsemblPlants 3885 PhaVulg1_0 GCA_000499845.1 2017-09-JGI N Y N Y Y Y phaseolus_vulgaris_core_51_104_1 1 +Physcomitrium patens physcomitrium_patens EnsemblPlants 3218 Phypa V3 GCA_000002425.2 2018-04-JGI N N Y Y Y Y physcomitrium_patens_core_51_104_2 1 +Pistacia vera pistacia_vera EnsemblPlants 55513 PisVer_v2 GCA_008641045.1 2019-10-EVM N N N Y Y N pistacia_vera_core_51_104_1 1 +Populus trichocarpa populus_trichocarpa EnsemblPlants 3694 Pop_tri_v3 GCA_000002775.3 2018-04-JGI N Y N Y Y Y populus_trichocarpa_core_51_104_3 1 +Prunus avium prunus_avium EnsemblPlants 42229 PAV_r1.0 GCA_002207925.1 2019-09-GDR N N N N N N prunus_avium_core_51_104_1 1 +Prunus dulcis prunus_dulcis EnsemblPlants 3755 ALMONDv2 GCA_902201215.1 2020-04-CNAG N N N Y Y N prunus_dulcis_core_51_104_1 1 +Prunus persica prunus_persica EnsemblPlants 3760 Prunus_persica_NCBIv2 GCA_000346465.2 2017-09-JGI N N N Y Y Y prunus_persica_core_51_104_2 1 +Quercus lobata quercus_lobata EnsemblPlants 97700 ValleyOak3.0 GCA_001633185.2 2020-05-UCLA N N N N N N quercus_lobata_core_51_104_1 1 +Rosa chinensis rosa_chinensis EnsemblPlants 74649 RchiOBHm-V2 GCA_002994745.2 2019-01-INRACNRS N N N Y Y N rosa_chinensis_core_51_104_1 1 +Saccharum spontaneum saccharum_spontaneum EnsemblPlants 62335 Sspon.HiC_chr_asm GCA_003544955.1 2019-08-UIL N N N Y Y N saccharum_spontaneum_core_51_104_1 1 +Selaginella moellendorffii selaginella_moellendorffii EnsemblPlants 88036 v1.0 GCA_000143415.1 2011-05-JGI N N Y Y Y Y selaginella_moellendorffii_core_51_104_1 1 +Sesamum indicum sesamum_indicum EnsemblPlants 4182 S_indicum_v1.0 GCA_000512975.1 2020-12-SINBASE N N N Y Y N sesamum_indicum_core_51_104_1 1 +Setaria italica setaria_italica EnsemblPlants 4555 Setaria_italica_v2.0 GCA_000263155.2 2015-11-JGI N N N Y Y Y setaria_italica_core_51_104_2 1 +Setaria viridis setaria_viridis EnsemblPlants 4556 Setaria_viridis_v2.0 GCA_005286985.1 2019-05-DOEJointGenomeInstitute N N N Y Y N setaria_viridis_core_51_104_1 1 +Solanum lycopersicum solanum_lycopersicum EnsemblPlants 4081 SL3.0 GCA_000188115.3 2017-02-SOL Y Y Y Y Y Y solanum_lycopersicum_core_51_104_3 1 +Solanum tuberosum solanum_tuberosum EnsemblPlants 4113 SolTub_3.0 GCA_000226075.1 2011-05-SolTub_3.0 N N N Y Y Y solanum_tuberosum_core_51_104_4 1 +Solanum tuberosum RH89-039-16 solanum_tuberosum_rh8903916 EnsemblPlants 4113 ASM1418947v1 GCA_014189475.1 2020-12-MSU N N N N N N solanum_tuberosum_rh8903916_core_51_104_1 1 +Sorghum bicolor sorghum_bicolor EnsemblPlants 4558 Sorghum_bicolor_NCBIv3 GCA_000003195.3 2017-06-JGI Y N N Y Y Y sorghum_bicolor_core_51_104_30 1 +Theobroma cacao Matina 1-6 theobroma_cacao EnsemblPlants 3641 Theobroma_cacao_20110822 GCA_000403535.1 2014-05-CGD N N N Y Y Y theobroma_cacao_core_51_104_1 1 +Theobroma cacao Belizian Criollo B97-61/B2 theobroma_cacao_criollo EnsemblPlants 3641 Criollo_cocoa_genome_V2 GCA_000208745.2 2019-03-CGH N N N Y Y N theobroma_cacao_criollo_core_51_104_1 1 +Trifolium pratense trifolium_pratense EnsemblPlants 57577 Trpr GCA_900079335.1 2016-04-TGAC N N N Y Y Y trifolium_pratense_core_51_104_1 1 +Triticum aestivum triticum_aestivum EnsemblPlants 4565 IWGSC GCA_900519105.1 2018-04-IWGSC Y Y N Y Y Y triticum_aestivum_core_51_104_4 1 +Triticum aestivum Arinalrfor triticum_aestivum_arinalrfor EnsemblPlants 4565 PGSBv2.0_Arinalrfor GCA_903993985.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_arinalrfor_core_51_104_1 1 +Triticum aestivum Cadenza triticum_aestivum_cadenza EnsemblPlants 4565 TGAC_cadenza GCA_902810645.1 2019-09-EI N N N N N N triticum_aestivum_cadenza_core_51_104_1 1 +Triticum aestivum Claire triticum_aestivum_claire EnsemblPlants 4565 TGAC_paragon GCA_902810655.1 2019-09-EI N N N N N N triticum_aestivum_claire_core_51_104_1 1 +Triticum aestivum Jagger triticum_aestivum_jagger EnsemblPlants 4565 PGSBv2.0_Jagger GCA_903993795.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_jagger_core_51_104_1 1 +Triticum aestivum Julius triticum_aestivum_julius EnsemblPlants 4565 PGSBv2.0_Julius GCA_903994195.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_julius_core_51_104_1 1 +Triticum aestivum Lancer triticum_aestivum_lancer EnsemblPlants 4565 PGSBv2.0_Lancer GCA_903993975.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_lancer_core_51_104_1 1 +Triticum aestivum Landmark triticum_aestivum_landmark EnsemblPlants 4565 PGSBv2.0_Landmark GCA_903995565.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_landmark_core_51_104_1 1 +Triticum aestivum Mace triticum_aestivum_mace EnsemblPlants 4565 PGSBv2.0_Mace GCA_903994175.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_mace_core_51_104_1 1 +Triticum aestivum Sy Mattis triticum_aestivum_mattis EnsemblPlants 4565 PGSBv2.0_Mattis GCA_903994185.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_mattis_core_51_104_1 1 +Triticum aestivum Norin61 triticum_aestivum_norin61 EnsemblPlants 4565 PGSBv2.0_Norin61 GCA_904066035.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_norin61_core_51_104_1 1 +Triticum aestivum Paragon triticum_aestivum_paragon EnsemblPlants 4565 EI_paragon GCA_902810665.1 2019-09-EI N N N N N N triticum_aestivum_paragon_core_51_104_1 1 +Triticum aestivum Robigus triticum_aestivum_robigus EnsemblPlants 4565 TGAC_robigus GCA_902810685.1 2019-09-EI N N N N N N triticum_aestivum_robigus_core_51_104_1 1 +Triticum aestivum Stanley triticum_aestivum_stanley EnsemblPlants 4565 PGSBv2.0_Stanley GCA_903994155.1 2019-07-PGSBv2.0 N N N N N N triticum_aestivum_stanley_core_51_104_1 1 +Triticum aestivum Weebill triticum_aestivum_weebil EnsemblPlants 4565 EI_WeebilV1 GCA_902810675.1 2016-05-TGAC N N N N N N triticum_aestivum_weebil_core_51_104_1 1 +Triticum dicoccoides triticum_dicoccoides EnsemblPlants 85692 WEWSeq v.1.0 GCA_002162155.1 2017-05-WEWSeq N Y N Y Y Y triticum_dicoccoides_core_51_104_1 1 +Triticum spelta triticum_spelta EnsemblPlants 58933 PGSBv2.0_Spelta GCA_903994165.1 2019-07-PGSBv2.0 N N N N N N triticum_spelta_core_51_104_1 1 +Triticum turgidum triticum_turgidum EnsemblPlants 4567 svevo GCA_900231445.1 2017-05-Svevo.v1 Y N N Y Y N triticum_turgidum_core_51_104_1 1 +Triticum urartu triticum_urartu EnsemblPlants 4572 ASM34745v1 GCA_000347455.1 2019-12-BGI N Y N Y Y Y triticum_urartu_core_51_104_1 1 +Vigna angularis vigna_angularis EnsemblPlants 3914 Vigan1.1 GCA_001190045.1 2015-08-BUA N Y N Y Y Y vigna_angularis_core_51_104_1 1 +Vigna radiata vigna_radiata EnsemblPlants 3916 Vradiata_ver6 GCA_000741045.2 2015-10-SNU N Y N Y Y Y vigna_radiata_core_51_104_2 1 +Vitis vinifera vitis_vinifera EnsemblPlants 29760 12X GCA_000003745.2 2012-07-CRIBI Y Y Y Y Y Y vitis_vinifera_core_51_104_3 1 +Zea mays zea_mays EnsemblPlants 4577 Zm-B73-REFERENCE-NAM-5.0 GCA_902167145.1 2019-12-CSHL Y Y N Y Y N zea_mays_core_51_104_8 1 diff --git a/supporting_files/zooma_ontologies.tsv b/supporting_files/zooma_ontologies.tsv.default similarity index 100% rename from supporting_files/zooma_ontologies.tsv rename to supporting_files/zooma_ontologies.tsv.default