The Biological Collections Ontology

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.

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.

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.

not sure if this should be a type of assay or a type of planned process

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.

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.

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).

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.

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.

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.

May want to work with OBI to define this term in a more general sense for investigations.

2/3/2009 Comment from OBI review.

Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications.

Request that IAO either clarify these or change definitions not to use them

The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

May be of the same or different species.

This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000080

This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000081.

Will be replaced by an external ontology class.

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.

This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.

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.

This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.

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.

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.

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).

This term has been replaced by OBI:specimen collection.

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.

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.

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.

This term has been replaced by OBI:specimen role.

Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.

Do not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.

At the GSC14 hackathon in 09/2012, we decided to deprecate this term.

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.

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.

Replaced by OBI organization. Request institution as synonym in OBI.

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.

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.

This term has been replaced by OBI:specimen.

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.

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.

If sampling is a OBI planned process, that captures that it is protocal governed.

Includes as output rubbings, casts, photographic prints, audio or video tapes.

Needs a better name. Current name is the definition.

Includes audio recordings and photographs (which are information artifacts).

Needs a better name. Current name is the definition.

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.

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.

The category of information pertaining to a logical set of records.

An action that occurs at some location during some time.

Container class for information about attributes related to a given sampling event.

The category of information pertaining to measurements associated with an event.

A preserved specimen that is a fossil.

Geological information, such as stratigraphy, that qualifies a region or place.

An output of a human observation process.

A taxonomic determination (e.g., the assignment to a taxon).

A specimen that is alive.

An output of a machine observation process.

A reference to or citation of one, a part of, or multiple specimens in scholarly publications.

A physical result of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.

A measurement of or fact about an rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource).

An existence of an Organism (sensu http://rs.tdwg.org/dwc/terms/Organism) at a particular place at a particular time.

The category of information pertaining to measurements accociated with an occurrence.

A particular organism or defined group of organisms considered to be taxonomically homogeneous.

A specimen that has been preserved.

A relationship of one rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource) to another.

Container class for information about the results of a sampling event (specimen, observation, etc.)

Container class for information about attributes related to a given sample.

Container class for information about the conditions and methods of acquisition of samples.

Container class for information about the location where a sampling event occurred.

A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.