This repository has been deprecated. Please see Bee Interaction Database for the active version.
Citation / Interaction Types / Data Definitions / Included Resources / Data Issues / Summary
bee-interaction-database is a repository for interaction and ecological trait data about bees (Hymenoptera). The observations are from the literature and focused on food, parasites, nesting biology, body size and other bee traits.
This GitHub repository was cloned from globalbioticinteractions/template-dataset, which includes a blank interactions.tsv, README and globi.json. GloBI requires that the interactions.tsv be called interactions.tsv and for the globi.json file to exist. Some column headers of inteteractions.tsv file was modified from the cloned template, but follow the naming conventions.
Seltmann, K., Van Wagner, J., Behm, R., Brown, Z., Tan, E., & Liu, K. (2020). BID: A project to share biotic interaction and ecological trait data about bees (Hymenoptera: Anthophila). UC Santa Barbara: Cheadle Center for Biodiversity and Ecological Restoration. Retrieved from https://escholarship.org/uc/item/1g21k7bf
The biotic species interactions in this dataset were mapped to terms in the Relations Ontology (RO). Biotic interactions are best viewed through Global Biotic Interactions
| interactionTypeName | interactionTypeId | description |
|---|---|---|
| visits | http://purl.obolibrary.org/obo/RO_0002618 | |
| visits flowers of | http://purl.obolibrary.org/obo/RO_0002622 | |
| eats | http://purl.obolibrary.org/obo/RO_0002470 | |
| (biotically) interacts with | http://purl.obolibrary.org/obo/RO_0002437 | An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. |
| ecologically co-occurs with | http://purl.obolibrary.org/obo/RO_0008506 | An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. |
| propertyTypeName | propertyTypeId |
|---|---|
| in nature | http://purl.obolibrary.org/obo/ENVO_01001226 |
| male | http://purl.obolibrary.org/obo/FBcv_0000333 |
| female | http://purl.obolibrary.org/obo/FBcv_0000334 |
| flower | http://purl.obolibrary.org/obo/PO_0009046 |
Presently, otherTraits are listed as a key:value list (delimited by semicolons). These include body size, nesting behavior, and any other traits that are not considered biotic interactions. Trait terms are following Encyclopedia of Life - TraitBank. Traits are defined as being either from the source or target taxon. They can be sourceGeneralObservation/targetGeneralObservation, which indicate overall study results, or sourceCommonKnowledge/targetCommonKnowledge, which indicates general knowledge about the taxon.
The definitions of the columns used in the interactions.tsv dataset are described here. If these correspond with Darwin Core they are mapped to those classes. Some of the columns in the template were unused.
- InteractionID : An non-unique identifier that links two interactions as part of the same observation in the dataset.
- basisOfRecord DWC:BasisOfRecord : The specific nature of the data record. For literature use LiteratureRecord.
- interactionText : The phrase or phrases copied verbatim from the text that describe the interaction.
- sourceTaxonId DWC:scientificNameID : An identifier for the nomenclatural (not taxonomic) details of a scientific name.
- sourceTaxonName DWC:scientificName : The lowest level taxonomic rank that can be determined.
- sourceVerbatimName : An OTU, morphospecies or other designation of the taxon.
- sourceFamilyName DWC:family : The family name of the source taxon.
- sourceCommonName DWC:vernacularName : common or vernacular name.
- sourceSexName DWC:sex : The sex of the biological individual(s) represented in the Occurrence.
- sourceSexID : Identifer for the sex name.
- sourceLifeStageName DWC:sex : TThe age class or life stage of the biological individual(s) at the time the Occurrence was recorded.
- sourceAssociatedSequences DWC:sex : list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.
- interactionTypeId : Identifier for the interaction type.
- interpretedInteractionTypeName : The name or term applied to the identifier of the interaction type as reported by the linked ontology.
- isNegated : This field is presently not supported in GloBI. It is intended to relate that a specific interaction was explicitly not observed.
- interactionTypeName : interaction type (ex. eats, piercing). The name of the interaction type should be the name as it is listed in the original text, which is not always the name of the term it is mapped to. As long as the definition to the mapping is compatible with the
interactionTypeName, it is usable as ainteractionTypeId. - targetBodyPartName : The specific name of the target body part. The name of the body part should be the name as it is listed in the original text, which is not always the name of the term it is mapped to. As long as the definition to the mapping is compatible with the
targetBodyPartName, it is usable as atargetBodyPartId. - targetBodyPartId : Identifer for the body part name.
- experimentalConditionName : ("in nature" - most common)
- experimentalConditionId :
- targetTaxonId DWC:scientificNameID : An identifier for the nomenclatural (not taxonomic) details of a scientific name.
- targetTaxonName DWC:scientificName : The lowest level taxonomic rank that can be determined.
- targetVerbatimName : An OTU, morphospecies or other designation of the taxon.
- targetFamilyName DWC:family : The family name of the source taxon.
- targetCommonName DWC:vernacularName : common or vernacular name.
- targetLifeStageName DWC:sex : TThe age class or life stage of the biological individual(s) at the time the Occurrence was recorded.
- targetAssociatedSequences DWC:sex : list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.
- country DWC:country : The name of the country or major administrative unit in which the Location occurs.
- stateProvince DWC:stateProvince : The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.
- county DWC:county : The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.
- verbatimLocality DWC:locality : The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description.
- locality DWC:locality : The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description.
- habitat DWC:habitat : category or description of the habitat in which the Event occurred.
- decimalLatitude DWC:decimalLatitude : The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.
- decimalLongitude DWC:decimalLongitude : The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.
- coordinateUncertaintyInMeters DWC:http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters : The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term.
- georeferenceRemarks DWC:http://rs.tdwg.org/dwc/terms/georeferenceRemarks : Notes or comments about the spatial description determination, explaining assumptions made in addition or opposition to the those formalized in the method referred to in georeferenceProtocol.
- minimumElevationInMeters DWC:minimumElevationInMeters : do not add zeros, if only one elevation add to maximumElevationInMeters
- maximumElevationInMeters DWC:maximumElevationInMeters : do not add zeros, if only one elevation add to maximumElevationInMeters
- verbatimEventDate DWC:eventDate : The verbatim original representation of the date and time information for an Event.
- eventDate DWC:eventDate : The date-time or interval during which an Event occurred.
- eventTime DWC:eventDate : The time or interval during which an Event occurred.
- otherTraits : key:value list (delimited by semicolons) for describing other traits. These include body size, nesting behavior, and any other traits that are not considered biotic interactions.
- containsTaxonTreatment : Does the paper contain taxon treatments? A taxon treatment is the scientific description of a taxon including a Latinized name of the nominate taxon, followed by one or several elements such as references to older literature citing this taxon and putting it in relation to the new information about the taxon being presented in the paper.
- TreatmentBankIdentifier : The identifer for the taxon treatment from TreatmentBank. A paper with a taxon treatment will need to be looked up in TreatmentBank for the TreatmentBank identifier.
- referenceDoi : This field was not populated in this dataset.
- referenceCitation : The reference for the interaction.
- referenceType : The type of reference.
- primarySource : Is the reference the primary source for the observation (TRUE/FALSE)? If it is not, include the primary source citation in the notes.
- primarySourceReference : If the reviewed article is not the primary source of the information (recorded as FALSE in primarySource) the citation for the primarySource is included here. If the reviewed article is the primary source this field is left blank.
- enteredBy : The person entering the data.
- notes : Notes about the database entry.
Literature used in this project is recorded on each record. If you have a new paper to add, please submit a new github issue or add it to the Bee Interaction Database group on Mendeley.
Interactions are focused at genus and below for bees. Other traits beside biotic interactions are included as a key:value pair in the other traits field. This field is presently descriptive.