find interactions related to a relatively long (~1k) list of taxa names

[jhpoelen]

as a taxonomist/scientist/ecologist, I'd like to get all the interactions within a specific taxonomic domain (e.g., all bees in North America, all fly pollinators and bee pollinators, any interaction related to fleas).

Currently, the GloBI tools include web search and the rglobi, both of which can be used comfortably up to 100.

For instance,

$ curl 'https://api.globalbioticinteractions.org/interaction.csv?sourceTaxon=Homo%20sapiens&sourceTaxon=Felis'
"source_taxon_external_id","source_taxon_name","source_taxon_path","source_specimen_occurrence_id","source_specimen_institution_code","source_specimen_collection_code","source_specimen_catalog_number","source_specimen_life_stage","source_specimen_basis_of_record","interaction_type","target_taxon_external_id","target_taxon_name","target_taxon_path","target_specimen_occurrence_id","target_specimen_institution_code","target_specimen_collection_code","target_specimen_catalog_number","target_specimen_life_stage","target_specimen_basis_of_record","latitude","longitude","study_title"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eats","NCBI:48155","Sylvia atricapilla","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Sauropsida | Sauria | Archelosauria | Archosauria | Dinosauria | Saurischia | Theropoda | Coelurosauria | Aves | Neognathae | Passeriformes | Sylvioidea | Sylviidae | Sylviinae | Sylvia | Sylvia atricapilla",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eats","NCBI:37595","Emberiza citrinella","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Sauropsida | Sauria | Archelosauria | Archosauria | Dinosauria | Saurischia | Theropoda | Coelurosauria | Aves | Neognathae | Passeriformes | Passeroidea | Fringillidae | Emberizinae | Emberizini | Emberiza | Emberiza citrinella",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eats","NCBI:48150","Phylloscopus collybita","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Sauropsida | Sauria | Archelosauria | Archosauria | Dinosauria | Saurischia | Theropoda | Coelurosauria | Aves | Neognathae | Passeriformes | Sylvioidea | Phylloscopidae | Phylloscopus | Phylloscopus collybita",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eats","NCBI:37595","Emberiza citrinella","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Sauropsida | Sauria | Archelosauria | Archosauria | Dinosauria | Saurischia | Theropoda | Coelurosauria | Aves | Neognathae | Passeriformes | Passeroidea | Fringillidae | Emberizinae | Emberizini | Emberiza | Emberiza citrinella",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eats","NCBI:48150","Phylloscopus collybita","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Sauropsida | Sauria | Archelosauria | Archosauria | Dinosauria | Saurischia | Theropoda | Coelurosauria | Aves | Neognathae | Passeriformes | Sylvioidea | Phylloscopidae | Phylloscopus | Phylloscopus collybita",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eats","NCBI:48155","Sylvia atricapilla","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Sauropsida | Sauria | Archelosauria | Archosauria | Dinosauria | Saurischia | Theropoda | Coelurosauria | Aves | Neognathae | Passeriformes | Sylvioidea | Sylviidae | Sylviinae | Sylvia | Sylvia atricapilla",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eatenBy","NCBI:452646","Neovison vison","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Caniformia | Mustelidae | Mustelinae | Neovison | Neovison vison",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"eatenBy","NCBI:452646","Neovison vison","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Caniformia | Mustelidae | Mustelinae | Neovison | Neovison vison",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"hostOf","no:match","IXODES COOLEI","IXODES | IXODES COOLEI",,,,,,,,,
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,,"hostOf","no:match","Spirometra mansonoides","Diphyllobothriidae",,,,,,,,,

To include all record level claims add "includeObservations=true", and retrieve of all the claims,

$ curl "https://api.globalbioticinteractions.org/interaction.csv?sourceTaxon=Homo%20sapiens&sourceTaxon=Felis&limit=10&includeObservations=true" 
"source_taxon_external_id","source_taxon_name","source_taxon_path","source_specimen_occurrence_id","source_specimen_institution_code","source_specimen_collection_code","source_specimen_catalog_number","source_specimen_life_stage","source_specimen_basis_of_record","interaction_type","target_taxon_external_id","target_taxon_name","target_taxon_path","target_specimen_occurrence_id","target_specimen_institution_code","target_specimen_collection_code","target_specimen_catalog_number","target_specimen_life_stage","target_specimen_basis_of_record","latitude","longitude","study_title"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"preservedSpecimen","adjacentTo","EOL:1081","Pulicidae","Animalia | Arthropoda | Insecta | Siphonaptera | Pulicoidea | Pulicidae","c8c79649-e31b-4aba-8688-eeec65bd4f64","UWM","WIRC","WIRC00146621","adult","preservedSpecimen",26.6406,-81.8723,"https://scan-bugs.org:443/portal/collections/individual/index.php?occid=57878815"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","NCBI:11834","RD114 retrovirus","root | Viruses | Riboviria | Pararnavirae | Artverviricota | Revtraviricetes | Ortervirales | Retroviridae | Orthoretrovirinae | Gammaretrovirus | unclassified Gammaretrovirus | RD114 retrovirus",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/21029758"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","NCBI:11292","Rabies lyssavirus","root | Viruses | Riboviria | Orthornavirae | Negarnaviricota | Haploviricotina | Monjiviricetes | Mononegavirales | Rhabdoviridae | Alpharhabdovirinae | Lyssavirus | Rabies lyssavirus",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/15297743"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","EOL_V2:741119","Parainfluenza virus 5","Viruses |  |  | Mononegavirales | Paramyxoviridae | Rubulavirus | Parainfluenza virus 5",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/23807746, 26583313, 28138777, 31450796"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","NCBI:75986","Mus dunni endogenous virus","root | Viruses | Riboviria | Pararnavirae | Artverviricota | Revtraviricetes | Ortervirales | Retroviridae | Orthoretrovirinae | Gammaretrovirus | Murine leukemia virus | unclassified Murine leukemia virus | Mus dunni endogenous virus",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/9696842"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","NCBI:1554500","Hervey virus","root | Viruses | Riboviria | Orthornavirae | Negarnaviricota | Haploviricotina | Monjiviricetes | Mononegavirales | Paramyxoviridae | Rubulavirinae | Pararubulavirus | Hervey pararubulavirus | Hervey virus",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/29390028"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature, RefSeq","hasPathogen","NCBI:1452540","Felis catus gammaherpesvirus 1","root | Viruses | Duplodnaviria | Heunggongvirae | Peploviricota | Herviviricetes | Herpesvirales | Herpesviridae | Gammaherpesvirinae | Percavirus | Felid gammaherpesvirus 1 | Felis catus gammaherpesvirus 1",,,,,,"Literature, RefSeq",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/26543105"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","NCBI:11772","Feline sarcoma virus","root | Viruses | Riboviria | Pararnavirae | Artverviricota | Revtraviricetes | Ortervirales | Retroviridae | Orthoretrovirinae | Gammaretrovirus | Feline leukemia virus | Feline sarcoma virus",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/6318314"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature","hasPathogen","NCBI:1379496","Feline kobuvirus","root | Viruses | Riboviria | Orthornavirae | Pisuviricota | Pisoniviricetes | Picornavirales | Picornaviridae | Kobuvirus | Aichivirus A | Feline kobuvirus",,,,,,"Literature",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/24786960"
"NCBI:9685","Felis catus","root | cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Laurasiatheria | Carnivora | Feliformia | Felidae | Felinae | Felis | Felis catus",,,,,,"Literature, UniProt","hasPathogen","NCBI:10243","Cowpox virus","root | Viruses | Varidnaviria | Bamfordvirae | Nucleocytoviricota | Pokkesviricetes | Chitovirales | Poxviridae | Chordopoxvirinae | Orthopoxvirus | Cowpox virus",,,,,,"Literature, UniProt",,,"Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016). Accessed at <ftp://ftp.genome.jp/pub/db/virushostdb/virushostdb.daily.tsv> on 10 Apr 2022.https://www.ncbi.nlm.nih.gov/pubmed/19828265"

[EMTuckerLab]

Test dataset to pull names attached
Sci-names.csv

[jhpoelen]

Knowing the limitations of web apis (unstable, hard to cite, and generally not recommended for use in scientific publications IMHO), you can scale up to say:

$ curl -L https://github.com/globalbioticinteractions/globalbioticinteractions/files/8534052/Sci-names.csv\
| tail -n+2\
| tr -d ','\
| sed 's+[ ]+%20+g'\
 > Sci-names.csv
$ cat Sci-names.csv\
 | sed 's+^+https://api.globalbioticinteractions.org/interaction.csv?includeObservations=true\&sourceTaxon=+g'\
 | xargs -L1 curl\
 > results-record-level.csv

where,

(1) curl -L https://github.com/globalbioticinteractions/globalbioticinteractions/files/8534052/Sci-names.csv - get the list of names posted earlier in this issue

(2) tail -n+2 - skip the first line to exclude the header

(3) tr -d ',' - delete all , characters

(4) sed 's+[ ]+%20+g'\ - replace whitespaces with %20 the url "special" character or escape character for a whitespace

(5) > Sci-names.csv save the results in a file called Sci-names.csv

(6) cat Sci-names.csv feeds the names of Sci-names.csv into step (7)

(7) sed 's+^+https://api.globalbioticinteractions.org/interaction.csv?includeObservations=true&sourceTaxon=+g' turns each name into a url request for individual record that make claims that involve the specified taxon.

(8) xargs -L1 curl - executes one request at a time using "curl" (command-line web browser)

(9) > results-...csv - save the results in a file called "result[something].csv"

If you'd like only get the results on taxon level, not on individual record level, you can omit the includeObservations=true like:

$ curl -L https://github.com/globalbioticinteractions/globalbioticinteractions/files/8534052/Sci-names.csv\
| tail -n+2\
| tr -d ','\
| sed 's+[ ]+%20+g'\
 > Sci-names.csv
$ cat Sci-names.csv\
 | sed 's+^+https://api.globalbioticinteractions.org/interaction.csv?sourceTaxon=+g'\
 | xargs -L1 curl\
 > results-taxon-level.csv

[jhpoelen]

Note how the linux "pipes" | are used to feed the output of one program into the input of the other. See https://en.wikipedia.org/wiki/Pipeline_%28Unix%29 .

the character \ is used to break up a single line of script across multiple rows to avoid super long lines.(see https://unix.stackexchange.com/questions/281309/shell-syntax-how-to-correctly-use-to-break-lines)

[jhpoelen]

and note that this kind of scripting would work for most macs, linux and windows with linux subsystem (see https://docs.microsoft.com/en-us/windows/wsl/about) .

Actually, you'd be able to run these program on your smart phone if only they let you access the terminal window.

[EMTuckerLab]

Follow up questions now that I'm doing this on my computer:

1. Do you know why the script/code for record level results would produce a basically empty file (see:
   results-record-level2.csv)? The code for taxon level only results works just fine...
2. How would I run these scripts for a different list or file, say one on my computer? Or does a list need to be loaded to GloBI in some fashion? Presumably not just adding a million different lists to search with onto this issue page - that would get excessive very fast :)
   Thanks!

[jhpoelen]

@EMTuckerLabUMMZ - thanks for the quick feedback questions!

re: 1 empty record level files - my bad! I forgot to escape the "&" in the sed command. I've updated the example in #782 (comment) . With the update, I was able to produce a 23MB results file. Please try again and confirm the fix works for you.

re: 2. you can use any list of names you'd like. One way would be to generate a text file with all your names, one per row, and then cat these into the example provided above. E.g., cat mynames.txt | sed ...

[jhpoelen]

@EMTuckerLabUMMZ if this doesn't make sense or doesn't work for you, I'd like to learn more about how I can help. Perhaps another videocall if desired?

[EMTuckerLab]

@jhpoelen
re: 1) Great - that works perfectly now too - thank you!
re: 2) I think I need more explanation on this one. I tried making a short .txt file list (see: test-names.txt ) on my computer and input the code as such:

$ curl -L https://github.com/globalbioticinteractions/globalbioticinteractions/files/8534052/Sci-names.csv\
| tail -n+2\
| tr -d ','\
| sed 's+[ ]+%20+g'\
> Sci-names.csv

$cat test-names.txt\
| sed 's+^+https://api.globalbioticinteractions.org/interaction.csv?sourceTaxon=+g'\
| xargs -L1 curl\
> results-Cremnops.csv

It didn't like that I has spaces and commas which weren't removed in the first part like before (can that be re-written?), but I just did a find and replace in the text doc. Then I reran the code as above. It produced a file, but it is all karbalygook (see: results-Cremnops.csv).
How should I have re-written the script? I'm guessing I need to change part of the first half somehow?
Thanks!

[jhpoelen]

@EMTuckerLabUMMZ nice! And thanks for sharing your sample data.

I ran:

curl -L https://github.com/globalbioticinteractions/globalbioticinteractions/files/8535061/test-names.txt

to retrieve:

Cremnops%montrealensis
Cremnops%vulgaris
Cremnops%californicus
Cremnops%desertor

and noticed that added the % character. If you'd like to escape the whitespace characters manually, you'd have to add 20 to complete the escaped whitespace in url land : %20 . I edited your file to do this and created test-names-2.txt and printed the content to the terminal using:

$ cat test-names-2.txt 
Cremnops%20montrealensis
Cremnops%20vulgaris
Cremnops%20californicus
Cremnops%20desertor

now, I ran the script to get results from globi's web api:

cat test-names-2.txt\
| sed 's+^+https://api.globalbioticinteractions.org/interaction.csv?sourceTaxon=+g'\
| xargs -L1 curl\
> test-names2-interactions.csv

and, in the last three lines (tail -n3) of this output file test-names2-interactions.csv, I saw:

$ cat test-names2-interactions.csv| tail -n3
"source_taxon_external_id","source_taxon_name","source_taxon_path","source_specimen_occurrence_id","source_specimen_institution_code","source_specimen_collection_code","source_specimen_catalog_number","source_specimen_life_stage","source_specimen_basis_of_record","interaction_type","target_taxon_external_id","target_taxon_name","target_taxon_path","target_specimen_occurrence_id","target_specimen_institution_code","target_specimen_collection_code","target_specimen_catalog_number","target_specimen_life_stage","target_specimen_basis_of_record","latitude","longitude","study_title"
"GBIF:1263231","Cremnops desertor","Animalia | Arthropoda | Insecta | Hymenoptera | Braconidae | Cremnops | Cremnops desertor",,,,,,,"hasParasite","GBIF:5801103","Perilampus microgastris","Animalia | Arthropoda | Insecta | Hymenoptera | Perilampidae | Perilampus | Perilampus microgastris",,,,,,,,,
"GBIF:1263231","Cremnops desertor","Animalia | Arthropoda | Insecta | Hymenoptera | Braconidae | Cremnops | Cremnops desertor",,,,,,,"hasParasite","GBIF:5801103","Perilampus microgastris","Animalia | Arthropoda | Insecta | Hymenoptera | Perilampidae | Perilampus | Perilampus microgastris",,,,,,,,,

Curious to see whether this trick also works for you. . .

test-names2-interactions.csv
test-names-2.txt

[EMTuckerLab]

@jhpoelen
Ah ha! Yes, that works just great! If only I had filled in the spaces properly the first time... 🙄 😄
Thanks!

[jhpoelen]

@EMTuckerLabUMMZ yeah, these computer programs are pretty finicky. That's why I like worked out copy-paste examples to start from, like all the neat examples you've collected on the https://globalbioticinteractions.org/how-to .