The Biological Collections Ontology
type: Ontology
imports: dwcterms.owl
imports: iao import.owl
imports: obi import.owl
imports: pco import.owl
imports: ontology-metadata.owl
imports: core.owl
contributor: Ramona Walls
contributor: John Wieczorek
contributor: Biocode Commons Ontology Hackathon members
contributor: John Deck
contributor: Barry Smith
contributor: Robert Guralnick
description: The BCO supports the interoperability of biodiversity and biodiversity related data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key aspect of the BCO is distinguishing among material samples (i.e. specimens), observing processes, and data about either of those entities.
license: http://creativecommons.org/publicdomain/zero/1.0/
comment: This is the editor's version of the ontology. Use with caution. For the live version of the ontology, use http://purl.obolibrary.org/obo/bco.owl. The Biological Collections Ontology was originally created at the Biocode Commons Hackathon at GSC14. Older versions can be viewed at http://code.google.com/p/biocode-commons/source/browse/#svn%2Ftrunk%2Fontologies%2Fbiocollections. Some of the classes in this ontology may be replaced by existing or newly requested terms from OBI or other ontologies.

taxonomic inventory metadata preferred name
type: AnnotationProperty
IAO_0000115: The label used in Humbolt Core.
sub property of: IAO_0000118

Axiom
annotated source: taxonomic inventory metadata preferred name
annotated property: IAO_0000115
annotated target: The label used in Humbolt Core.
source: ecog.02942

BCO preferred label
type: AnnotationProperty
IAO_0000115: The label preferred for use with this ontology. To be added only with imported terms.

obsolete has role
type: ObjectProperty
IAO_0000115: The relationship between an independent continuant and a role. Slightly more specific than the parent class bearer of.
IAO_0000231: IAO_0000423
comment: This property was originally created in OBI, but in OBI it was deprecated and replaced by BFO:0000087. However, BFO:0000087 was replaced by 'has role at some time', which is not yet part of a stable release. Once the BFO role has been tested and released, it may replace 'has role' in both BCO and OBI. There are currently two versions of 'has role', the old one from BFO (which is used in OBI's definition of specimen) and the RO version. For consistency with OBI, we have used the BFO relation in BCO, but this should be resolved at a higher level.
deprecated: true

obsolete derives from by planned process
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
IAO_0000231: IAO_0000423
deprecated: true

obsotlete is derived into by planned process
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
IAO_0000116: This property used an old version of the has input relation, so it has been deprecated.
IAO_0000231: IAO_0000423
deprecated: true

to taxon
type: ObjectProperty
sub property of: IAO_0000136
domain: identification assertion
range: Taxon
IAO_0000115: A relation used to link a taxonomic association to a taxon. Should be used with the of organism relation.

of organism
type: ObjectProperty
sub property of: IAO_0000136
domain: identification assertion
range: PCO_0000031
IAO_0000115: A relation used to link an identification association to an organismal entity. Should be used together with the to taxon relation.

member of taxon
type: ObjectProperty
sub property of: BFO_0000050
property chain axiom:
  inverse of: of organism
property chain axiom: to taxon
IAO_0000115: A shortcut relation from an organsimal entity to a taxon.

is_specified_input_of
type: ObjectProperty

observing process
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000293
  some values from: BFO_0000040
subclass of: Restriction
  on property: OBI_0000299
  some values from: IAO_0000030
taxonomic inventory metadata preferred name: sighting
IAO_0000112: A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
IAO_0000112: Observing and recording the presence or absence of butterflies during a transect walk.
IAO_0000112: Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
IAO_0000114: IAO_0000125
IAO_0000115: A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
IAO_0000116: This class replaces class bco_0000003, which was made obsolete because of identifier format.
IAO_0000116: We are having conversation with OBI developers about how this term relates to OBI:assay (). Is it equivalent, broader, narrower? What does it mean to be the input to an observation.
creator: Biocode Commons Ontology Hackathon
comment: An observing process is distinguished from a specimen collecting process in by having an information content entity as an output rather than a specimen. The information artifact may be written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, which is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.

submitting process
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: OBI_0000299
  some values from: BFO_0000040
IAO_0000112: a curator submitting a herbarium speciman to a museum
IAO_0000112: a researcher submitting a water sample to a laboratory storage collection
IAO_0000114: IAO_0000428
IAO_0000115: A planned process whereby a person submits a material sample to an organization.
IAO_0000116: false
creator: Biocode Commons Ontology Hackathon

locality description
type: Class
subclass of: IAO_0000030
IAO_0000114: IAO_0000428
IAO_0000115: An information artifact that is about a spatio-temporal region at which a process (such as collecting process, observing process, or material sampling process) occured.
IAO_0000116: This term replaces the obsolete class bco_0000025, but with the correct identifier format.
creator: Biocode Commons Ontology Hackathon
comment: Darwin Core needs to describe both the site and time where some activity occurred as an information content entity (e.g., in recording data from a lab notebook),therefore, we made locality description about a spatial temporal region, rather than a site.

museum collection
type: Class
subclass of: object aggregate
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0100051
IAO_0000112: The herbarium collection at the New York Botanical Garden.
IAO_0000112: the painting collection at the Louvre Museum
IAO_0000114: IAO_0000428
IAO_0000115: An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
IAO_0000116: This term replaced bco_0000031, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon
comment: Intent is to document biodiversity for research and education. The class museum collection has meaning that is much broader than biological collections. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum collection.

organismal museum collection
type: Class
subclass of: museum collection
IAO_0000112: the insect collection at the Smithsonian Institution
IAO_0000114: IAO_0000428
IAO_0000115: A museum collection that has as member part a material sample that was derived from an organism.
IAO_0000116: This term replaced bco_0000032, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

taxonomic identification process
type: Class
equivalent class: Identification
subclass of: OBI_0000011
IAO_0000112: Associating a museum specimen with a specific taxonomic concept based on its characters.
IAO_0000112: Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
IAO_0000112: Using DNA barcoding to identify a plant species.
IAO_0000112: Using a key to identify a plant in the field.
IAO_0000114: IAO_0000125
IAO_0000115: A planned process by which an organismal entity is associated with a taxon or taxa.
IAO_0000116: Need to add a relation for has specified output some taxonomic association.
IAO_0000116: This term replaces bco_0000042, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

material target of observation
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000087
    some values from: material target of observation role
subclass of: BFO_0000040
IAO_0000112: A bird observed during a Christmas Bird Count
IAO_0000112: A bird observed during a transect walk.
IAO_0000112: A lizard observed in the field that is not collected but whose location is recorded in a field notebook.
IAO_0000112: A tree is forest plot that is measured for diameter at breast height (DBH).
IAO_0000114: IAO_0000428
IAO_0000115: A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
IAO_0000116: This term replaces bco_0000044, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

material target of observation role
type: Class
equivalent class: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: BFO_0000054
    some values from: observing process
subclass of: BFO_0000023
IAO_0000112: the role borne by a bird during a Christmas Bird Count
IAO_0000114: IAO_0000125
IAO_0000115: A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
IAO_0000116: This term replaced bco_0000046, which was made obsolete because of incorrect identifier format.
creator: Biocode Commons Ontology Hackathon

taxonomic inventory process
type: Class
equivalent class: Class
  intersection of: observing process
  intersection of: Restriction
    on property: OBI_0000299
    some values from: taxonomic inventory
taxonomic inventory metadata preferred name: inventory type
IAO_0000114: IAO_0000124
IAO_0000115: A planned process by which a taxonomic inventory is created.
creator: Taxonomic Inventory Metadata Workshop
comment: not sure if this should be a type of assay or a type of planned process

Axiom
annotated source: taxonomic inventory process
annotated property: IAO_0000115
annotated target: A planned process by which a taxonomic inventory is created.
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

taxonomic inventory
type: Class
equivalent class: Class
  intersection of: IAO_0000030
  intersection of: Restriction
    on property: OBI_0000312
    some values from: taxonomic inventory process
subclass of: IAO_0000030
IAO_0000112: "The Flora of North America"
IAO_0000112: The butterflies of Great Britain
IAO_0000112: The plants of Yosemite National Park
IAO_0000114: IAO_0000125
IAO_0000115: A list of names ascribed to biological entities of specified organismal scope recorded over some defined spatial and temporal scope following a described sampling protocol and sampling effort, potentially including values indicating abundance or biomass of the biological entities
creator: Taxonomic Inventory Metadata Workshop
source: https://docs.google.com/spreadsheet/ccc
comment: The biological entities are almost always species and the organismal scope typically a taxon but potentially also an ecologically or functionally defined grouping (e.g. ‘water birds’ or ‘trees’) or other operational unit (e.g. genes). The list would typically contain multiple entities, but may be as short as a single entity or, if a sampling effort focused on a certain taxon yielded no results, even contain none.

restricted search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: restricted search
IAO_0000112: Pollard transect-- "walk a 1km transect at a slow&steady pace, and report on all TOI within 5m in front, and 2.5m on either side of you."
IAO_0000114: IAO_0000122
IAO_0000115: A taxonomic inventory process that is restricted to plots, transects, or points, in which a person or group of people is comprehensively covering the entire area, usually with a well-described survey time or pace. The search is restricted to a defined and human-scale geospatial area (usually traversable within a time course of less than a day) within which there is an expectation of a comprehensive accounting of the taxonomic items of interest.
creator: Taxonomic Inventory Metadata Workshop

Axiom
annotated source: restricted search taxonomic inventory process
annotated property: IAO_0000115
annotated target: A taxonomic inventory process that is restricted to plots, transects, or points, in which a person or group of people is comprehensively covering the entire area, usually with a well-described survey time or pace. The search is restricted to a defined and human-scale geospatial area (usually traversable within a time course of less than a day) within which there is an expectation of a comprehensive accounting of the taxonomic items of interest.
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

open search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: open search
IAO_0000112: Individual Christmas Bird Count by some team. Organized field trip to a State Park.
IAO_0000114: IAO_0000122
IAO_0000115: A taxonomic inventory process in which the search is restricted within a larger defined geographic area, but where effort isn't even or complete across the region, and thus not a comprehensive accounting of taxa of interest. Temporal duration is typically longer than restricted searches, lasting hours to several days.
creator: Taxonomic Inventory Metadata Workshop

Axiom
annotated source: open search taxonomic inventory process
annotated property: IAO_0000115
annotated target: A taxonomic inventory process in which the search is restricted within a larger defined geographic area, but where effort isn't even or complete across the region, and thus not a comprehensive accounting of taxa of interest. Temporal duration is typically longer than restricted searches, lasting hours to several days.
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

opportunistic search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: opportunistic search
IAO_0000112: Many E-Bird lists are of this nature; useful supplementary information is that observers should state whether they documented every taxon of interest they saw.
IAO_0000114: IAO_0000122
IAO_0000115: A taxonomic inventory process that is a more casual reporting of occurrences of taxa of interest, still intended to be a comprehensive accounting of the taxa of interest, but with no pre-specified investment of effort nor planned trajectory for discovery, thus of often idiosyncratic length or spatial scope.
creator: Taxonomic Inventory Metadata Workshop
comment: This is more typically used to report multiple sightings, where the motivation is to record presence and abundance, rather than for individual anecdotal occurrences that are noteworthy.

Axiom
annotated source: opportunistic search taxonomic inventory process
annotated property: IAO_0000115
annotated target: A taxonomic inventory process that is a more casual reporting of occurrences of taxa of interest, still intended to be a comprehensive accounting of the taxa of interest, but with no pre-specified investment of effort nor planned trajectory for discovery, thus of often idiosyncratic length or spatial scope.
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

trap or sample taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: trap or sample inventory
IAO_0000112: an inventory of insects in a area using pheremone traps
IAO_0000112: an inventory of the large mammals of a park based on camera traps
IAO_0000112: inventories based on trawl samples
IAO_0000114: IAO_0000122
IAO_0000115: A taxonomic inventory process that is typically restricted in geospatial extent that involves either the physical extraction of some evidence of the presence of the taxa of interest, such as a whole organisms, scat, fur, other material samples or information artifacts such as photographs or sound recordings
creator: Taxonomic Inventory Metadata Workshop
comment: Can be highly targeted and or baited (pheromone trap), or general (pitfall). Trap events can either be "triggered" but of long-term deployment, or rigorously temporally specified (left out overnight).

Axiom
annotated source: trap or sample taxonomic inventory process
annotated property: IAO_0000115
annotated target: A taxonomic inventory process that is typically restricted in geospatial extent that involves either the physical extraction of some evidence of the presence of the taxa of interest, such as a whole organisms, scat, fur, other material samples or information artifacts such as photographs or sound recordings
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

adventitious taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: incidental or adventitious inventory
IAO_0000112: data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
IAO_0000114: IAO_0000122
IAO_0000115: A taxonomic inventory process in which taxon occurrences are recorded as co-variates of another study, or by happenstance, and later compiled as a taxonomic inventory.
creator: Taxonomic Inventory Metadata Workshop

Axiom
annotated source: adventitious taxonomic inventory process
annotated property: IAO_0000115
annotated target: A taxonomic inventory process in which taxon occurrences are recorded as co-variates of another study, or by happenstance, and later compiled as a taxonomic inventory.
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

compilation taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
taxonomic inventory metadata preferred name: compilation inventory
IAO_0000112: Atlases and Checklists
IAO_0000114: IAO_0000124
IAO_0000115: A taxonomic inventory process in which a list of taxa of interest is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
creator: Taxonomic Inventory Metadata Workshop
comment: A compiliation taxonomic inventory process is typically required to document the occurences of taxa of interest over large geospatial areas, or to derive the most comprehensive accounting of presence and absence of taxa of interest in a larger region.

Axiom
annotated source: compilation taxonomic inventory process
annotated property: IAO_0000115
annotated target: A taxonomic inventory process in which a list of taxa of interest is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
IAO_0000119: http://onlinelibrary.wiley.com/doi/10.1111/ecog.02942/full

museum
type: Class
subclass of: OBI_0000245
subclass of: Restriction
  on property: BFO_0000051
  some values from: museum collection
IAO_0000112: The Louvre Museum
IAO_0000112: The Smithsonian Institution
IAO_0000114: IAO_0000122
IAO_0000115: An institution that cares for (conserves) a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance.
IAO_0000119: ISBN:9780759105096
comment: A museum may make its collections available for public viewing through exhibits that may be permanent or temporary. The class museum has meaning that is much broader than biological collecitons. It may be better to import this term from another, more general ontology and create a specific subclass for natural history museum.

obsolete fossil specimen
type: Class
subclass of: Obsolete Class
IAO_0000112: a fossil housed in a natural history museum
IAO_0000115: A specimen that is derived from a fossil.
IAO_0000231: IAO_0000103
deprecated: true

obsolete living specimen
type: Class
subclass of: Obsolete Class
IAO_0000112: a bacterial culture in a culture collection
IAO_0000112: a tree in an arboretum
IAO_0000112: an animal in a zoo
IAO_0000112: germplasm
IAO_0000115: A specimen that is alive.
IAO_0000231: IAO_0000103
deprecated: true

obsolete preserved specimen
type: Class
subclass of: Obsolete Class
IAO_0000115: A specimen that has been preserved.
IAO_0000231: IAO_0000103
deprecated: true

obsolete darwin core class
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
deprecated: true

human observation process
type: Class
subclass of: observing process
IAO_0000112: a biologist recording an observation of an animal in a field notebook
IAO_0000112: an entomologist recording the presense of butterflies while walking a transect
IAO_0000114: IAO_0000123
IAO_0000115: An observing process in which the observing entity consists of one or more humans.
comment: May be able to use the has agent = has active participant relationship for defining this. May want to work with OBI to define this term in a more general sense for investigations.

machine observation process
type: Class
subclass of: observing process
IAO_0000112: a camera trap recording the presence of a jaguar
IAO_0000112: a sensor periodically recording the surface temperature of a leaf over several hours
IAO_0000114: IAO_0000123
IAO_0000115: An observing process in which the observing entity consists of one or more machines.
comment: May want to work with OBI to define this term in a more general sense for investigations.

identification assertion
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: to taxon
  some values from: Taxon
subclass of: Restriction
  on property: of organism
  some values from: PCO_0000031
IAO_0000115: A data item that is the output of a taxonomic identification process and associates some organismal entity with a taxon or taxa.
IAO_0000119: PPO hackathon Sep. 2016.

object aggregate
type: Class
subclass of: BFO_0000040

object
type: Class
subclass of: BFO_0000040

organism or virus or viroid
type: Class
subclass of: BFO_0000040
IAO_0000115: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
IAO_0000117: Melissa Haendel
IAO_0000412: Common Anatomy Reference Onotology - CARO2
IAO_0000589: organism or virus
IAO creation date: 9/18/11

OBI_0000659
type: Class
BCO preferred label: specimen collection process

OBI_0100051
type: Class
equivalent class: MaterialSample
IAO_0000112: A herbarium or museum specimen.
IAO_0000112: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.

obsolete evidence role
type: Class
subclass of: Obsolete Class
IAO_0000112: A museum specimen that serves as evidence for a taxonomic identification process bears an evidence role.
IAO_0000115: A role that is borne by some entity as a result of the entity providing evidence to support an assertion.
IAO_0000231: IAO_0000423
comment: Will be replaced by an external ontology class.
deprecated: true

obsolete persistent evidence role
type: Class
subclass of: Obsolete Class
IAO_0000115: An evidence role that persists through time.
comment: Could add relation that persistant evidence role is specifically dependent on a museum material samples. Deprecated because we do not need this term. Can use OBI:evidence role. Not clear what it means for an evidence role to persist through time.
deprecated: true

obsolete collecting process
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000227
comment: This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
deprecated: true

obsolete observing process
type: Class
subclass of: Obsolete Class
taxonomic inventory metadata preferred name: sighting
IAO_0000112: A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
IAO_0000112: Observing and recording the presence or absence of butterflies during a transect walk.
IAO_0000112: Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
IAO_0000115: A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
IAO_0000116: This class was made obsolete because of the incorrect identifier format. It has been replaced by BCO_0000003.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
comment: The information artifact may written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, and is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.
deprecated: true

obsolete being there process
type: Class
subclass of: Obsolete Class
IAO_0000115: A process of existing in a particular spatio-temporal region.
IAO_0000231: IAO_0000103
comment: This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.
deprecated: true

obsolete printed report
type: Class
subclass of: Obsolete Class
IAO_0000112: a book
IAO_0000112: a field notebook
IAO_0000114: IAO_0000124
IAO_0000231: IAO_0000423
creator: Biocode Commons Ontology Hackathon
comment: IAO has the term document, which is defined as "A collection of information content entities intended to be understood together as a whole" and has as examples journal article, patent application, laboratory notebook, and book. IAO also has a term for report, but it is not defined. With this term, we want to describe the physical object that corresponds to some information content entity, together with the information content contained in the document or report. This class may be less important for modeling collection data, but could be important for efforts to get hand written (specifically dependent) reports into an electronic (generically dependent) report, and monitoring that process.
deprecated: true

obolete printed observational report
type: Class
subclass of: obsolete printed report
IAO_0000112: A field notebook.
IAO_0000114: IAO_0000124
IAO_0000115: A printed report that records the outcome of some observing process.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete selecting process
type: Class
subclass of: Obsolete Class
IAO_0000112: Filtering sea water to extract only organisms smaller than a certain size.
IAO_0000112: deciding which branch to collect for a herbarium specimen
IAO_0000115: A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
IAO_0000231: IAO_0000423
creator: Biocode Commons Ontology Hackathon
comment: The criteria for selection may be specified in a protocol or may be ad hoc. Should be replaced by OBI:selection, but first OBI needs to fix the definition.
deprecated: true

obsolete submitting process
type: Class
subclass of: Obsolete Class
IAO_0000112: a curator submitting a herbarium speciman to a museum
IAO_0000112: a researcher submitting a water sample to a laboratory storage collection
IAO_0000115: A planned process whereby a person submits a material sample to an organization.
IAO_0000116: This term was made obsolete because it had the incorrect identifier format. It has been replaced by BCO_0000016.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete physical extraction process
type: Class
subclass of: Obsolete Class
IAO_0000112: picking leaves from a plant
IAO_0000112: removing a fish from the ocean with a net
IAO_0000112: removing dna from cells
IAO_0000115: A process that involves removing a material entity from its original site to another site.
IAO_0000231: IAO_0000423
creator: Biocode Commons Ontology Hackathon
comment: Considered acquisition in OBI, but that is about taking possession. Physical extraction may involve taking pocession, but it may also just involve extraction of something that is already posessed (e.g. of dna from cells).
deprecated: true

obsolete material sampling process
type: Class
subclass of: Obsolete Class
IAO_0000112: collecting plant parts for herbarium specimens
IAO_0000112: collecting sea water samples as part of Ocean Sampling Day
IAO_0000115: A planned process that includes selecting a material entity for study, physically extracting the material entity, and submitting the material entity to some institution for preservation or study.
IAO_0000118: collecting event
IAO_0000231: IAO_0000103
creator: Biocode Commons Ontology Hackathon
comment: This term has been replaced by OBI:specimen collection.
deprecated: true

obsolete data sampling process
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete statistical sampling process
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete locality description
type: Class
subclass of: Obsolete Class
IAO_0000115: An information artifact that is about a spatio-temporal region at which a process (such as collecting process, observing process, or material sampling process) occured.
IAO_0000116: This term was deprecated because it has the wrong ID format. It is replaced by BCO_0000025.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
comment: Darwin Core needs to describe both the site and time where some activity occurred as an information content entity (e.g., in recording data from a lab notebook),therefore, we made locality description about a spatial temporal region, rather than a site.
deprecated: true

obsolete material sample role
type: Class
subclass of: Obsolete Class
IAO_0000112: the role borne by a branch when it becomes a herbarium specimen
IAO_0000115: A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
IAO_0000231: IAO_0000103
creator: Biocode Commons Ontology Hackathon
comment: This term has been replaced by OBI:specimen role.
deprecated: true

obsolete successful material sampling process
type: Class
subclass of: Obsolete Class
IAO_0000115: A sampling process that has as output some material sample.
IAO_0000231: IAO_0000103
comment: Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.
deprecated: true

obsolete unsuccessful material sampling process
type: Class
subclass of: Obsolete Class
IAO_0000115: A material sampling process that has as output exactly zero material samples.
IAO_0000231: IAO_0000103
comment: Do not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.
deprecated: true

obsolete museum collection entity
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
comment: At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
deprecated: true

obsolete organismal museum collection entity
type: Class
subclass of: obsolete museum collection entity
IAO_0000115: A museum collections entity that derives from an organismal entity, has a persistent evidence role and 'depends on' a process of collecting.
IAO_0000231: IAO_0000103
comment: The label for this on the original diagram was 'collection object'. However, not all entities in collections will fit the defition of 'object', so 'collection entity is probably a better name. The relation 'depends on' cannot really be used here. Old BFO has 'inverse depends on', but this is not in the current BFO. See dwc_bfo2_new.owl for the original logical definition. At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
deprecated: true

obsolete museum collection
type: Class
subclass of: Obsolete Class
IAO_0000112: The herbarium collection at the New York Botanical Garden.
IAO_0000112: the painting collection at the Louvre Museum
IAO_0000114: IAO_0000428
IAO_0000115: An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
IAO_0000116: This term was made obsolete because of incorrect identifier format. It has been replaced by BCO_0000031.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
comment: Intent is to document biodiversity for research and education. The class museum collection has meaning that is much broader than biological collections. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum collection.
deprecated: true

obsolete organismal museum collection
type: Class
subclass of: Obsolete Class
IAO_0000112: the insect collection at the Smithsonian Institution
IAO_0000114: IAO_0000428
IAO_0000115: A museum collection that has as member part a material sample that was derived from an organism.
IAO_0000116: This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000031.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete institution
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000423
comment: Replaced by OBI organization. Request institution as synonym in OBI.
deprecated: true

obsolete organismal entity
type: Class
subclass of: obsolete taxonomic identification process
IAO_0000115: A material entity that derives from an organism or virus or viroid.
comment: This class is understood to mean: A material entity that is either an organism, a part of an organism, a collection of organisms, or a fossil. The relation 'organismal entity derives from organism' was in the original diagram. Subclasses of organismal entity include organism, and It is not clear if it is valid to that an organism derives from an organism (is the derives from relation reflexive?). At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
deprecated: true

obsolete organism or virus or viroid
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000423
comment: This terms was replaced by a term imported from CARO. The original diagram only had organsim, but DWC and GOs both need to include viruses and viroids.
deprecated: true

obsolete material sample
type: Class
subclass of: Obsolete Class
IAO_0000112: A herbarium or museum specimen.
IAO_0000112: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
IAO_0000115: A material entity that has a material sample role. A material entity takes on the material sample role by being the output of a material samping process. That is, is selected for study, collected, and submitted to an institution for preservation or study.
IAO_0000231: IAO_0000103
creator: Biocode Commons Ontology Hackathon
comment: This term has been replaced by OBI:specimen.
deprecated: true

obsolete data sample
type: Class
subclass of: Obsolete Class
IAO_0000115: An information content entity (?) that is the result of some data sampling process.
IAO_0000231: IAO_0000103
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete statistical sample
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
deprecated: true

obsolete protocol governed sampling activity
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
comment: If sampling is a OBI planned process, that captures that it is protocal governed.
deprecated: true

obsolete taxonomic identification process
type: Class
subclass of: Obsolete Class
IAO_0000112: Associating a museum specimen with a specific taxonomic concept based on its characters.
IAO_0000112: Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
IAO_0000112: Using DNA barcoding to identify a plant species.
IAO_0000112: Using a key to identify a plant in the field.
IAO_0000115: A process by which a material sample is associated with a taxon or taxa.
IAO_0000116: This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000042.
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete process that yields a material representation of a material entity
type: Class
subclass of: Obsolete Class
IAO_0000116: This term was made obsolete because of incorrect identifier format. It should be replaced by an external ontology term.
IAO_0000231: IAO_0000423
IAO_0000232: Consider term from OBI or IAO.
creator: Biocode Commons Ontology Hackathon
comment: Includes as output rubbings, casts, photographic prints, audio or video tapes. Needs a better name. Current name is the definition.
deprecated: true

obsolete material target of observation
type: Class
subclass of: Obsolete Class
IAO_0000112: A bird observed during a Christmas Bird Count
IAO_0000112: A bird observed during a transect walk.
IAO_0000112: A tree is forest plot that is measured for diameter at breast height (DBH).
IAO_0000112: An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
IAO_0000115: A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
IAO_0000116: This term was made obsolete because of incorrected identifier format. It is replaced by BCO_0000044.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

obsolete process that yields an information artifact that is a representation of a material entity
type: Class
subclass of: Obsolete Class
IAO_0000116: This term was made obsolete because of incorrect identifier format. It should be replaced by an external ontology term.
IAO_0000231: IAO_0000423
IAO_0000232: Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
creator: Biocode Commons Ontology Hackathon
comment: Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
deprecated: true

obsolete material target of observation role
type: Class
subclass of: Obsolete Class
IAO_0000112: the role borne by a bird during a Christmas Bird Count
IAO_0000115: A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
IAO_0000116: This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000046.
IAO_0000231: incorrect identifier format, replaced
creator: Biocode Commons Ontology Hackathon
deprecated: true

zooarcheological specimen
type: Class
subclass of: PreservedSpecimen
IAO_0000112: A set of gastropod and bivalve shells found in shell midden from an archaeological site in Alaska.
IAO_0000115: A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some animal.
IAO_0000119: Rob Guralnick
comment: Zooarchaeological specimens are typically collections of biological material generated as part of an archaeological collecting process that is separate from the type of processes that would yield other kinds of samples or collections of samples. This process almost always entails collecting in-situ from archaeological sites where there is evidence of past human material culture.

archeobotanical specimen
type: Class
subclass of: PreservedSpecimen
IAO_0000112: Preserved seeds found in a storage jar at an archeological site.
IAO_0000115: A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some plant.
IAO_0000119: Rob Guralnick
comment: Archaeologicalbotanical specimens are typically collections of biological material generated as part of an archaeological collecting process that is separate from the type of processes that would yield other kinds of samples or collections of samples. This process almost always entails collecting in-situ from archaeological sites where there is evidence of past human material culture.

obsolete zooarcheological specimen
type: Class
subclass of: Obsolete Class
IAO_0000112: A set of gastropod and bivalve shells found in shell midden from an archaeological site in Alaska.
IAO_0000115: A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some animal.
IAO_0000119: Rob Guralnick
IAO_0000231: incorrect identifier format, replaced
comment: This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000080
deprecated: true

obsolete archeobotanical specimen
type: Class
subclass of: Obsolete Class
IAO_0000112: Preserved seeds found in a storage jar at an archeological site.
IAO_0000115: A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some plant.
IAO_0000119: Rob Guralnick
IAO_0000231: incorrect identifier format, replaced
comment: This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000081.
deprecated: true

VocabularyEncodingScheme
type: Class
subclass of: Obsolete Class
IAO_0000231: IAO_0000103
deprecated: true

Location
type: Class
BCO preferred label: location of an event
IAO_0000114: IAO_0000123
IAO_0000424: The site where a process occurs. In the context of Dawrin Core, this is generally where a specimen is collected, an organism is observed or a measurement is taken.

Event
type: Class
BCO preferred label: event

FossilSpecimen
type: Class
subclass of: PreservedSpecimen
BCO preferred label: fossil specimen

HumanObservation
type: Class
subclass of: IAO_0000027
BCO preferred label: human observation

Identification
type: Class
BCO preferred label: identification
IAO_0000114: IAO_0000125

LivingSpecimen
type: Class
subclass of: OBI_0100051
BCO preferred label: living specimen

MachineObservation
type: Class
subclass of: IAO_0000027
BCO preferred label: machine observation

MaterialSample
type: Class
BCO preferred label: specimen

MeasurementOrFact
type: Class
subclass of: Obsolete Class
IAO_0000231: This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
deprecated: true

Organism
type: Class
subclass of: PCO_0000031
BCO preferred label: organism

PreservedSpecimen
type: Class
subclass of: OBI_0100051
BCO preferred label: preserved specimen

ResourceRelationship
type: Class
subclass of: Obsolete Class
IAO_0000231: This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
deprecated: true

Taxon
type: Class
subclass of: PCO_0000000
BCO preferred label: taxon

Obsolete Class
type: Class
subclass of: Thing

specimen collection process X
type: NamedIndividual

material entity A
type: NamedIndividual
is_specified_input_of: specimen collection process X

material entity B
type: NamedIndividual
is_specified_input_of: specimen collection process Y
OBI_0000312: specimen collection process X

material entity C
type: NamedIndividual
OBI_0000312: specimen collection process Y

specimen collection process Y
type: NamedIndividual

incorrect identifier format, replaced
type: NamedIndividual
type: IAO_0000078
comment: false

obsolete incorrect identifier format, do not use
type: NamedIndividual
IAO_0000231: incorrect identifier format, replaced
deprecated: true

FossilSpecimen

OBI_0000112
IAO_0000118: material sample

Event
deprecated: false
IAO_0000114: IAO_0000428

GeologicalContext
BCO preferred label: geological context
IAO_0000114: IAO_0000124

Occurrence
IAO_0000116: This Darwin Core class should not be used when annotating data with BCO. It is not mapped to BCO classes because its meaning is too ambiguous.
BCO preferred label: occurrence

dwc_terms status