Study design - RDFBones/FrNonMetricTraits GitHub Wiki

The study design is a bundle of information that is used to define a specific type of investigation. It provides answers to the following questions. What material is suitable for this type of investigation? Which assays are carried out? What kinds of data are collected? Therefore, a detailed study design lies at the heart of every extension.

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Protocol

According to the OBI ontology, a protocol is defined as follows:

“A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.”

In case of FrNonMetricTraits, the data entry form used at Biological Anthropology Freiburg is regarded as protocol. Together with the other information summarized in the study design, researchers should be able to reliably reproduce the data collection process.

Assay specifications

In the OBI ontology, assays are understood as the smallest units of scientific analysis. Thus, assessing cranial and mandibular non-metric traits means carrying out assays. In fact, assays are part of the study design execution and not part of the study design. The study design just contains several instances of the class 'Investigation assay specification’.

While the protocol contains information on what non-metric traits should be recorded, the assay specifications contain exact definitions of the relevant traits taken from Hauser & DeStefano 1989 as well as common synonyms used for these traits.

Specimen collection objectives

In general, a specimen collection objective just advises the researcher to obtain material which is a potential input for the respective assay, i. e. a potential specimen (see data collection). Thus, it does not define a specific specimen collection procedure. On the contrary, there may be several different specimen collection procedures which may satisfy the same specimen collection objective.

But what exactly is a "potential specimen"? In case of the Inca Bone, a Neurocranium is a potential specimen. Neurocranium was selected for additional suture bones because suture bones are by definition not present on another bone - they are additional flat bones found on a cranium. Thus, the input of the SpecimenCollectionProcess.IncaBone is restricted to Neurocranium. In case of the Mental Foramen, a mandible is a potential specimen since there may be no or multiple foramina present on a mandible. In this way, the specimen collection process defined in the FrNonMetricTraits ontology fulfills the corresponding specimen collection objective. See specimen collection for further information.

Skeletal material requirements

While the restrictions on the input of the specimen collection process determine which skeletal elements are potential specimen, for example a Neurocranium in the case of the Inca Bone, the skeletal material requirements specify in which state the skeletal elements should be preserved. In the skeletal inventories, two kinds of states of skeletal elements are recorded: completeness in two states and taphonomic state. For example, the ValueSpecification.IncaBone has the label 'complete'. Hence, the skeletal elements that are potential specimen should be 'complete' and not 'partly present'. See specimen collection for further information.

Specification of generated data

In a FrNonMetricTraits investigation, only one type of data is generated: presence data. A presence datum is a categorical measurement datum which has exactly one of the following LabelForPresence: 'not observable', present, absent.