Biocode Commons Ontology Hackathon members
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.
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
The label preferred for use with this ontology. To be added only with imported terms.
BCO preferred label
The relationship between an independent continuant and a role. Slightly more specific than the parent class bearer of.
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.
obsolete has role
obsolete derives from by planned process
This property used an old version of the has input relation, so it has been deprecated.
obsotlete is derived into by planned process
A relation used to link a taxonomic association to a taxon. Should be used with the of organism relation.
to taxon
A relation used to link an identification association to an organismal entity. Should be used together with the to taxon relation.
of organism
A shortcut relation from an organsimal entity to a taxon.
member of taxon
sighting
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.
Observing and recording the presence or absence of butterflies during a transect walk.
Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
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.
This class replaces class bco_0000003, which was made obsolete because of identifier format.
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.
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.
observing process
a curator submitting a herbarium speciman to a museum
a researcher submitting a water sample to a laboratory storage collection
A planned process whereby a person submits a material sample to an organization.
submitting process
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.
This term replaces the obsolete class bco_0000025, but with the correct identifier format.
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.
locality description
The herbarium collection at the New York Botanical Garden.
the painting collection at the Louvre Museum
An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
This term replaced bco_0000031, which was made obsolete because of incorrect identifier format.
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.
museum collection
the insect collection at the Smithsonian Institution
A museum collection that has as member part a material sample that was derived from an organism.
This term replaced bco_0000032, which was made obsolete because of incorrect identifier format.
organismal museum collection
Associating a museum specimen with a specific taxonomic concept based on its characters.
Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
Using DNA barcoding to identify a plant species.
Using a key to identify a plant in the field.
A planned process by which an organismal entity is associated with a taxon or taxa.
Need to add a relation for has specified output some taxonomic association.
This term replaces bco_0000042, which was made obsolete because of incorrect identifier format.
taxonomic identification process
A bird observed during a Christmas Bird Count
A lizard observed in the field that is not collected but whose location is recorded in a field notebook.
A tree is forest plot that is measured for diameter at breast height (DBH).
A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
This term replaces bco_0000044, which was made obsolete because of incorrect identifier format.
material target of observation
the role borne by a bird during a Christmas Bird Count
A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
This term replaced bco_0000046, which was made obsolete because of incorrect identifier format.
material target of observation role
inventory type
A planned process by which a taxonomic inventory is created.
not sure if this should be a type of assay or a type of planned process
taxonomic inventory process
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
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.
taxonomic inventory
restricted search
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."
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.
restricted search taxonomic inventory process
open search
Individual Christmas Bird Count by some team. Organized field trip to a State Park.
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.
open search taxonomic inventory process
opportunistic search
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.
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.
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.
opportunistic search taxonomic inventory process
trap or sample inventory
an inventory of insects in a area using pheremone traps
an inventory of the large mammals of a park based on camera traps
inventories based on trawl samples
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
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).
trap or sample taxonomic inventory process
incidental or adventitious inventory
data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
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.
adventitious taxonomic inventory process
compilation inventory
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.
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.
compilation taxonomic inventory process
The Louvre Museum
The Smithsonian Institution
An institution that cares for (conserves) a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance.
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.
museum
a fossil housed in a natural history museum
A specimen that is derived from a fossil.
obsolete fossil specimen
a bacterial culture in a culture collection
a tree in an arboretum
an animal in a zoo
germplasm
A specimen that is alive.
obsolete living specimen
A specimen that has been preserved.
obsolete preserved specimen
obsolete darwin core class
a biologist recording an observation of an animal in a field notebook
an entomologist recording the presense of butterflies while walking a transect
An observing process in which the observing entity consists of one or more humans.
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.
human observation process
a camera trap recording the presence of a jaguar
a sensor periodically recording the surface temperature of a leaf over several hours
An observing process in which the observing entity consists of one or more machines.
May want to work with OBI to define this term in a more general sense for investigations.
machine observation process
A data item that is the output of a taxonomic identification process and associates some organismal entity with a taxon or taxa.
identification assertion
object aggregate
object
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
Common Anatomy Reference Onotology - CARO2
organism or virus
A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
A museum specimen that serves as evidence for a taxonomic identification process bears an evidence role.
A role that is borne by some entity as a result of the entity providing evidence to support an assertion.
Will be replaced by an external ontology class.
obsolete evidence role
An evidence role that persists through time.
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.
obsolete persistent evidence role
This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
obsolete collecting process
This class was made obsolete because of the incorrect identifier format. It has been replaced by BCO_0000003.
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.
obsolete observing process
A process of existing in a particular spatio-temporal region.
This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.
obsolete being there process
a book
a field notebook
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.
obsolete printed report
A printed report that records the outcome of some observing process.
obolete printed observational report
Filtering sea water to extract only organisms smaller than a certain size.
deciding which branch to collect for a herbarium specimen
A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
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.
obsolete selecting process
This term was made obsolete because it had the incorrect identifier format. It has been replaced by BCO_0000016.
obsolete submitting process
removing a fish from the ocean with a net
A process that involves removing a material entity from its original site to another site.
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).
obsolete physical extraction process
collecting plant parts for herbarium specimens
collecting sea water samples as part of Ocean Sampling Day
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.
collecting event
This term has been replaced by OBI:specimen collection.
obsolete material sampling process
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.
obsolete data sampling process
obsolete statistical sampling process
This term was deprecated because it has the wrong ID format. It is replaced by BCO_0000025.
obsolete locality description
the role borne by a branch when it becomes a herbarium specimen
A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
This term has been replaced by OBI:specimen role.
obsolete material sample role
A sampling process that has as output some material sample.
Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.
obsolete successful material sampling process
A material sampling process that has as output exactly zero material samples.
Do not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.
obsolete unsuccessful material sampling process
At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
obsolete museum collection entity
A museum collections entity that derives from an organismal entity, has a persistent evidence role and 'depends on' a process of collecting.
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.
obsolete organismal museum collection entity
This term was made obsolete because of incorrect identifier format. It has been replaced by BCO_0000031.
obsolete museum collection
This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000031.
obsolete organismal museum collection
Replaced by OBI organization. Request institution as synonym in OBI.
obsolete institution
A material entity that derives from an organism or virus or viroid.
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.
obsolete organismal entity
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.
obsolete organism or virus or viroid
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.
This term has been replaced by OBI:specimen.
obsolete material sample
An information content entity (?) that is the result of some data sampling process.
obsolete data sample
obsolete statistical sample
If sampling is a OBI planned process, that captures that it is protocal governed.
obsolete protocol governed sampling activity
A process by which a material sample is associated with a taxon or taxa.
This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000042.
obsolete taxonomic identification process
This term was made obsolete because of incorrect identifier format. It should be replaced by an external ontology term.
Consider term from OBI or IAO.
Includes as output rubbings, casts, photographic prints, audio or video tapes. Needs a better name. Current name is the definition.
obsolete process that yields a material representation of a material entity
An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
This term was made obsolete because of incorrected identifier format. It is replaced by BCO_0000044.
obsolete material target of observation
Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
obsolete process that yields an information artifact that is a representation of a material entity
This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000046.
obsolete material target of observation role
A set of gastropod and bivalve shells found in shell midden from an archaeological site in Alaska.
A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some animal.
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.
zooarcheological specimen
Preserved seeds found in a storage jar at an archeological site.
A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some plant.
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.
archeobotanical specimen
This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000080
obsolete zooarcheological specimen
This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000081.
obsolete archeobotanical specimen
location of an event
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
fossil specimen
human observation
identification
living specimen
machine observation
specimen
This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
organism
preserved specimen
taxon
specimen collection process X
material entity A
material entity B
material entity C
specimen collection process Y
incorrect identifier format, replaced
obsolete incorrect identifier format, do not use
material sample
geological context
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.
dwc_terms status