Returns data frame with supported data fields
Usage
get_data_fields(opts = list(), read_csv = read_csv_online)Examples
# \donttest{
get_data_fields()
#> name
#> 1 latitude
#> 2 longitude
#> 3 altitude
#> 4 footprintWKT
#> 5 locality
#> 6 event_date
#> 7 study_title
#> 8 interaction_type
#> 9 target_taxon_name
#> 10 source_taxon_name
#> 11 target_taxon_common_names
#> 12 source_taxon_common_names
#> 13 target_taxon_external_id
#> 14 source_taxon_external_id
#> 15 target_taxon_path
#> 16 source_taxon_path
#> 17 target_taxon_path_ranks
#> 18 source_taxon_path_ranks
#> 19 target_taxon_path_ids
#> 20 source_taxon_path_ids
#> 21 target_specimen_frequency_of_occurrence
#> 22 target_specimen_frequency_of_occurrence_percent
#> 23 target_specimen_total_volume_ml
#> 24 target_specimen_total_volume_ml_percent
#> 25 target_specimen_total_count
#> 26 target_specimen_total_count_percent
#> 27 tmp_and_unique_target_specimen_id
#> 28 tmp_and_unique_source_specimen_id
#> 29 target_specimen_occurrence_id
#> 30 source_specimen_occurrence_id
#> 31 target_specimen_catalog_number
#> 32 source_specimen_catalog_number
#> 33 target_specimen_institution_code
#> 34 source_specimen_institution_code
#> 35 target_specimen_collection_code
#> 36 source_specimen_collection_code
#> 37 target_specimen_physiological_state
#> 38 target_specimen_physiological_state_id
#> 39 source_specimen_physiological_state
#> 40 source_specimen_physiological_state_id
#> 41 target_specimen_body_part
#> 42 target_specimen_body_part_id
#> 43 source_specimen_body_part
#> 44 source_specimen_body_part_id
#> 45 source_specimen_life_stage
#> 46 source_specimen_life_stage_id
#> 47 target_specimen_life_stage
#> 48 target_specimen_life_stage_id
#> 49 source_specimen_sex
#> 50 source_specimen_sex_id
#> 51 target_specimen_sex
#> 52 target_specimen_sex_id
#> 53 source_specimen_basis_of_record
#> 54 target_specimen_basis_of_record
#> 55 taxon_name
#> 56 taxon_common_names
#> 57 taxon_external_id
#> 58 taxon_external_url
#> 59 taxon_path
#> 60 taxon_path_ids
#> 61 taxon_path_ranks
#> 62 study_url
#> 63 study_doi
#> 64 study_citation
#> 65 study_source_citation
#> 66 study_source_id
#> 67 number_of_distinct_taxa
#> 68 number_of_distinct_taxa_no_match
#> 69 number_of_sources
#> 70 number_of_studies
#> 71 number_of_interactions
#> 72 study_source_doi
#> 73 study_source_format
#> 74 study_source_archive_uri
#> 75 study_source_last_seen_at
#> description
#> 1 Same as DwC decimalLatitude (http://rs.tdwg.org/dwc/terms/decimalLatitude).
#> 2 Same as DwC decimalLongitude (http://rs.tdwg.org/dwc/terms/decimalLongitude).
#> 3 Similar to elevation and expressed in meters. Negative altitude describes depth related to sea level.
#> 4 Same as DwC footprintWKT (http://rs.tdwg.org/dwc/terms/footprintWKT).
#> 5 Same as DwC locality (http://rs.tdwg.org/dwc/terms/locality).
#> 6 Same as DwC eventDate (http://rs.tdwg.org/dwc/terms/eventDate).
#> 7 Internal non-unique identifier used to refer to a specific claim, or group of claims.
#> 8 A human readable description of the interaction . This is the verb (or predicate) that connects the source (or subject) with their target (or object). Also known as "interaction_type_name" (e.g., "eats"). See also the machine readable URI counterpart (interaction_type_id, e.g., "http://purl.obolibrary.org/obo/RO_0002470").
#> 9 Most granular taxonomic name of the object of the interaction (subject -> source, object -> target). Same as DwC scientificName (http://rs.tdwg.org/dwc/terms/scientificName) may not include authorship. If the subject or object not an organism, this may describe an abiotic interaction partner (e.g., "vehicle", "pack of cigarettes").
#> 10 Most granular taxonomic name of the subject of the interaction (subject -> source, object -> target). Same as DwC scientificName (http://rs.tdwg.org/dwc/terms/scientificName) may not include authorship. If the subject or object not an organism, this may describe an abiotic interaction partner (e.g., "vehicle", "pack of cigarettes").
#> 11 Common (or vernacular) name describing the interaction target (or object). Same as DwC vernacularName (http://rs.tdwg.org/dwc/terms/vernacularName). Maybe a list delimited by pipes "|" where names may be suffixed by their language code (e.g., "humans @en | mens @nl | mensch @de").
#> 12 Common (or vernacular) name describing the interaction source (or subject). Same as DwC vernacularName (http://rs.tdwg.org/dwc/terms/vernacularName). Maybe a list delimited by pipes "|" where names may be suffixed by their language code (e.g., "humans @en | mens @nl | mensch @de").
#> 13 Single existing identifier associated with the taxonomic name of the target. Ids are prefixed using the schemes documented in https://api.globalbioticinteractions.org/prefixes (e.g., NCBI:9606 refers to NCBI's Taxon ID relating to Homo sapiens). Same as DwC taxonID (http://rs.tdwg.org/dwc/terms/taxonID).
#> 14 Single existing identifier associated with the taxonomic name of the source. Ids are prefixed using the schemes documented in https://api.globalbioticinteractions.org/prefixes (e.g., NCBI:9606 refers to NCBI's Taxon ID relating to Homo sapiens). Same as DwC taxonID (http://rs.tdwg.org/dwc/terms/taxonID).
#> 15 Pipe limited list of name hierarchy related to the target taxon name. Only includes elements from a single taxonomic resource. Same as DwC HigherTaxon (http://rs.tdwg.org/dwc/terms/HigherTaxon) E.g., \\"cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Euarchontoglires | Primates | Haplorrhini | Simiiformes | Catarrhini | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens" for the name hierarchy related to NCBI:9606 Homo sapiens . Note that for abiotic names, this may include a hierarchy defined by some ontology. E.g. plastic as defined by ENVO:01000404 may have hierarchy including ("environmental material | anthropogenic environmental material | ... | plastic").
#> 16 Pipe limited list of name hierarchy related to the source taxon name. Only includes elements from a single taxonomic resource. Same as DwC HigherTaxon (http://rs.tdwg.org/dwc/terms/HigherTaxon) E.g., \\"cellular organisms | Eukaryota | Opisthokonta | Metazoa | Eumetazoa | Bilateria | Deuterostomia | Chordata | Craniata | Vertebrata | Gnathostomata | Teleostomi | Euteleostomi | Sarcopterygii | Dipnotetrapodomorpha | Tetrapoda | Amniota | Mammalia | Theria | Eutheria | Boreoeutheria | Euarchontoglires | Primates | Haplorrhini | Simiiformes | Catarrhini | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens" for the name hierarchy related to NCBI:9606 Homo sapiens.
#> 17 Pipe delimited list of taxonomic ranks of the target taxon hierarchy. E.g., NCBI's Homo sapiens NCBI:9606 ("| superkingdom | clade | kingdom | clade | clade | clade | phylum | subphylum | clade | clade | clade | clade | superclass | clade | clade | clade | class | clade | clade | clade | superorder | order | suborder | infraorder | parvorder | superfamily | family | subfamily | genus | species") where empty values represent undefined or unknown ranks.
#> 18 Pipe delimited list of taxonomic ranks of the source taxon hierarchy. E.g., NCBI's Homo sapiens NCBI:9606 ("| superkingdom | clade | kingdom | clade | clade | clade | phylum | subphylum | clade | clade | clade | clade | superclass | clade | clade | clade | class | clade | clade | clade | superorder | order | suborder | infraorder | parvorder | superfamily | family | subfamily | genus | species") where empty values represent undefined or unknown ranks.
#> 19 Pipe delimited list of taxonomic identifiers of the target taxon hierarchy. E.g., NCBI's Homo sapiens NCBI:9606 "NCBI:131567 | NCBI:2759 | NCBI:33154 | NCBI:33208 | NCBI:6072 | NCBI:33213 | NCBI:33511 | NCBI:7711 | NCBI:89593 | NCBI:7742 | NCBI:7776 | NCBI:117570 | NCBI:117571 | NCBI:8287 | NCBI:1338369 | NCBI:32523 | NCBI:32524 | NCBI:40674 | NCBI:32525 | NCBI:9347 | NCBI:1437010 | NCBI:314146 | NCBI:9443 | NCBI:376913 | NCBI:314293 | NCBI:9526 | NCBI:314295 | NCBI:9604 | NCBI:207598 | NCBI:9605 | NCBI:9606" .
#> 20 Pipe delimited list of taxonomic identifiers of the source taxon hierarchy. E.g., NCBI's Homo sapiens NCBI:9606 "NCBI:131567 | NCBI:2759 | NCBI:33154 | NCBI:33208 | NCBI:6072 | NCBI:33213 | NCBI:33511 | NCBI:7711 | NCBI:89593 | NCBI:7742 | NCBI:7776 | NCBI:117570 | NCBI:117571 | NCBI:8287 | NCBI:1338369 | NCBI:32523 | NCBI:32524 | NCBI:40674 | NCBI:32525 | NCBI:9347 | NCBI:1437010 | NCBI:314146 | NCBI:9443 | NCBI:376913 | NCBI:314293 | NCBI:9526 | NCBI:314295 | NCBI:9604 | NCBI:207598 | NCBI:9605 | NCBI:9606" .
#> 21 Frequency at which the interaction between source and target was observed.
#> 22 Relative frequency of occurrence of a specific interaction between souce and target relating to interactions with other targets. E.g., this bee visited 10% flowers of X and 90% flower of Y. coupled with a study or group of observation events.
#> 23 Total volume of the stomach of the source (or subject).
#> 24 Percentage of the stomach volume occupied by the specimen of classified by the target. (e.g., a stomach of an Atlantic cod contained 25% crabs. (source: Atlantic cod, target: crab).
#> 25 Absolute number of observations that documented the interaction of between source/target individuals (e.g., this bee visited that flower 14 times).
#> 26 Relative number of observations that documented the interaction between source/target individuals (e.g., this bee visited that flower 40% of the time).
#> 27 GloBI internal identifier for target (or object) record (e.g., a record describing a specimen acted as the target (or subject) of the interaction).
#> 28 GloBI internal identifier for source (or subject) record (e.g., a record describing a specimen acted as the target (or subject) of the interaction).
#> 29 External identifier for target (or object) record (e.g., http://arctos.database.museum/guid/DMNS:Mamm:18530). Similar to http://rs.tdwg.org/dwc/terms/occurrenceID .
#> 30 External identifier for source (or subject) record (e.g., http://arctos.database.museum/guid/DMNS:Mamm:18530). Similar to http://rs.tdwg.org/dwc/terms/occurrenceID .
#> 31 External catalogue number for target (or object) record (e.g., "DMNS:Mamm:18703"). Similar to http://rs.tdwg.org/dwc/terms/catalogNumber .
#> 32 External catalogue number for source (or subject) record (e.g., "DMNS:Mamm:18703"). Similar to http://rs.tdwg.org/dwc/terms/catalogNumber .
#> 33 External institution code for target (or object) record (e.g., "DMNS"). Similar to http://rs.tdwg.org/dwc/terms/institutionCode.
#> 34 External institution code for source (or subject) record (e.g., "DMNS"). Similar to http://rs.tdwg.org/dwc/terms/institutionCode.
#> 35 External collection code for target (or object) record (e.g., "Mamm"). Similar to http://rs.tdwg.org/dwc/terms/institutionCode.
#> 36 External collection code for source (or subject) record (e.g., "Mamm"). Similar to http://rs.tdwg.org/dwc/terms/institutionCode.
#> 37 Description of physiological state of the target (or object) of the interaction (e.g., "dead", "alive".
#> 38 External identifier for physiological state of the target (or object) of the interaction (e.g., "http://purl.obolibrary.org/obo/PATO_0001422" identifies "dead").
#> 39 Description of physiological state of the source (or subject) of the interaction (e.g., "dead", "alive".
#> 40 External identifier for physiological state of the source (or subject) of the interaction (e.g., "http://purl.obolibrary.org/obo/PATO_0001422" identifies "dead").
#> 41 Description of the body part of the target (or object) participating in the interaction (e.g., "hand", "leg").
#> 42 External identifier of the body part of the target (or object) participating in the interaction (e.g., "http://purl.obolibrary.org/obo/UBERON_0002398" identifies "manus" or "hand"
#> 43 Description of the body part of the target (or object) participating in the interactions (e.g., "hand", "leg").
#> 44 External identifier of the body part of the source (or subject) participating in the interaction (e.g., "http://purl.obolibrary.org/obo/UBERON_0002398" identifies "manus" or "hand"
#> 45 Description of the life stage of the source (or subject) participating in the interaction (e.g., "juvenile", "adult"
#> 46 External identifier of the life stage of the source (or subject) participating in the interaction (e.g., "http://purl.obolibrary.org/obo/UBERON_0034919" identifies "juvenile stage")
#> 47 Description of the life stage of the target (or object) participating in the interaction (e.g., "juvenile", "adult"
#> 48 External identifier of the life stage of the target (or object) participating in the interaction (e.g., "http://purl.obolibrary.org/obo/UBERON_0034919" identifies "juvenile stage")
#> 49 Sex of the source (or subject) participating in the interaction (e.g., "male", "female"
#> 50 External identifier of the sex of the source (or subject) participating in the interaction (e.g., "http://purl.obolibrary.org/obo/UBERON_0003101" identifies "male organism")
#> 51 Sex of the target (or object) participating in the interaction (e.g., "male", "female"
#> 52 External identifier of the sex of the source (or subject) participating in the interaction (e.g., "http://purl.obolibrary.org/obo/UBERON_0003101" identifies "male organism")
#> 53 Describes how the source (or subject) information was obtained. Similar to http://rs.tdwg.org/dwc/terms/basisOfRecord.
#> 54 Describes how the target (or object) information was obtained. Similar to http://rs.tdwg.org/dwc/terms/basisOfRecord.
#> 55 most granular taxonomic name (e.g., "Homo sapiens")
#> 56 Pipe delimited list of common (or vernacular) names associated with a taxonomic name followed by @<language code> (e.g., "human @en | Mensch @de").
#> 57 Existing identifier associated with a taxonomic name (e.g., "NCBI:9606").
#> 58 Existing url associated with a taxonomic name (e.g., "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606")
#> 59 Pipe delimited list of taxonomic hierarchy associated with a taxonomic name (e.g., "Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens").
#> 60 pipe delimited list of taxonomic hierarchy identifiers associated with a taxonomic name (e.g., "ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:180089 | ITIS:943773 | ITIS:943778 | ITIS:943782 | ITIS:180090 | ITIS:943805 | ITIS:180091 | ITIS:180092")
#> 61 "Kingdom | Subkingdom | Infrakingdom | Phylum | Subphylum | Infraphylum | Superclass | Class | Subclass | Infraclass | Order | Suborder | Infraorder | Superfamily | Family | Subfamily | Genus | Species"
#> 62 URL associated with the recorded interaction claim (e.g., "http://www.stoppinginvasives.org/dotAsset/6d3c1060-971d-4e12-bf0e-9d34aefb998c.pdf").
#> 63 DOI associated with the recorded interaction claim (e.g., "10.2317/JKES0811.17.1").
#> 64 Citation associated with the recorded interaction claim. (e.g., "Kern, W.H. (2004). Dealing with Iguanas in the South Florida Landscape: ENY-714/IN528, 8/2004. EDIS, 2004(15).")
#> 65 Citation associated with the datasets containing the recorded interaction claim. (e.g., "Sabina E. Vlad, Jodey Peyton & Sofie Meeus. 2022. Interactions data on *Iguana iguana* and other taxa from the Cayman Islands.")
#> 66 Internal identifier (or namespace) for dataset containing the recorded interaction claim. (e.g., "globalbioticinteractions/jeught2021").
#> 67 only available for /reports/* queries
#> 68 only available for /reports/* queries
#> 69 only available for /reports/* queries
#> 70 only available for /reports/* queries
#> 71 available for /interaction queries by source/target taxon name and/or interactionType only
#> 72 DOI (i.e., https://doi.org) associated with the datasets containing the recorded interaction claim (e.g., "10.5281/zenodo.1436853").
#> 73 format of the dataset containing the recorded interaction claim (e.g., "dwca")
#> 74 URI of the datasets containing the recorded interaction claim (e.g., https://zenodo.org/record/1436853/files/globalbioticinteractions/template-dataset-0.0.3.zip)
#> 75 date/time in ISO8601 describing when the dataset containing the recorded interaction claim was last seen. (e.g., "2022-05-06T14:30:42.917Z")
# }