Specimen collection
Specimen collection (obo:OBI_00000659) is a process undertaken to procure material to be analysed in an investigation. With osteological projects, this usually involves screening of the available material to ascertain if all elements are appropriate for study. Reasons for exclusions might be insufficient material preservation (coded in data items of type :TaphonomicStateDatum) or completeness (:CompletenessDatum). Which elements go into an investigation has a strong influence on its outcome, so it needs to be thoroughly documented.
But specimen collection can go beyond the mere selection of skeletal material. It might involve probing of skeletal elements, i.e. the removal of tissue for analytical processes. In this case, the specimen is just the probe that was extracted. Also, several skeletal elements might be needed to establish one specimen. For example, research on skeletal joints might involve all articular surfaces forming a joint. In this case, the specimen collection process would have several skeletal elements (the articular surfaces) as input, but only one specimen (the joint) as output. In other scenarios, several specimen could be extracted from one skeletal element, e.g. when slicing a tooth into a series of thin sections for TCA analysis.
The criteria for the inclusion or exclusion of material in a specimen collection process are defined as specimen collection objectives (class obo:OBI_0001896) which are part of the study design. Also part of the study design can be skeletal material requirements (class :SkeletalMaterialRequirements) that define skeletal elements that are needed to carry out a certain type of investigation. Their counterparts are plan specifications of type :SkeletalMaterialSpecification, which are defined with the plan that concretises a study design for use with a specific investigation.
Skeletal material specifications refer to skeletal inventories which describe the skeletal material that is to be analysed in an invenstigation. Skeletal inventories are made up of a series of measurement data, each referring to a specific segment of some skeletal element. Skeletal material requirements, on the other side, have specifications of measurement data as might appear in skeletal inventories. For a part of skeletal material to be put up as input to an investigation, the type of measurement datum specified by the skeletal material requirement needs to appear in the skeletal inventories defined by the skeletal material specification AND the value of the measurement datum needs to be within the range specified by the value specification of the skeletal material requirement.
A software like RDFBones can automatically perform this matching process in order to identify elements in skeletal inventories that satisfy the skeletal material requirements defined for a certain specimen collection process. If several skeletal material requirements are defined, all of these have to be met before any input for specimen collection is defined.
So the slection process works in two stages:
- automatic selection of skeletal inventories that formally comply with the material requirements
- the actual specimen collection process, based on the specified specimen collection objectives and typically carried out by and investigator
Stage one defines input for specimen collection processes, stage two their output. As the first stage is an automated process, the specifications involved need to be formulated in a way that preempts the creation of false negatives. It is the objective in stage two to identify and document false positives.
Figure: General structure of the specimen collection process (cf. key to symbols in network graphs).
Input to a specimen collection process (object property obo:OBI_0000293 'has_specified_input') could be any number of any continuant (obo:BFO_0000002), which includes all of human physical anatomy. If the specimen collection process selects skeletal material, input is always defined on the basis of class :SegmentOfSkeletalElement. This is necessary to ensure correct matching of skeletal material requirements and specifications. As segments can be defined in software extensions, they are useful to generate extremely specific information on the qualities of skeletal elements.
NOTE:
Class obo:OBI_0000659 ('Specimen collection process') has the following restriction:
'has_specified_input' some 'material entity'
For use in RDFBones, this restriciton has to be extended to class obo:BFO_0000002 ('Continuant') in order to include the class :SegmentOfSkeletal Element, which is not a subclass of class obo:BFO_0000040 ('Material entity').
Any element that is specified as an input to the process can potentially contribute to its output, i.e. be included in the investigation. All output of a specimen collection process are referred to as specimen (class obo:OBI_0100051, cf. page Investigation execution). Material that is excluded from an investigation is input to a specimen collection process but does not contribute to its output. Still, an instance of class obo:OBI_0000659 ('Specimen collection process') is created for any input and information on reasons for exclusion are stored with this instance.
Figure: Implementation of an extension, following the general structure above (cf. key to symbols in network graphs).
Figure: Example of a skeletal material specification not matching the specifications of the skeletal material requirement. No input for specimen collection is defined (cf. key to symbols in network graphs).
Figure: Example of a skeletal material specification matching the specifications of the skeletal material requirement. An instance representing a specimen collection process is automatically created and linked to the input material (cf. key to symbols in network graphs).
