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Updated README, footer links, and intro text
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| <section class="introductory"> | ||
| <p>This is the Term Resolution page for NIDM-Experiment (NIDM-E), meaning that each term in NIDM-E has a URI that can be referred to when the term is used in a semantic web application. For example, <a href="#blooddraw">https://incf-nidash.github.io/nidm-experiment/index.html#blooddraw</a> points to the entry on this page for the term nidm:blooddraw, in the nidm namespace.</p> | ||
| <p>NIDM-E is a controlled terminology that can be used to describe neuroscience-related experiments. While NIDM-E was initially constructed to describe MRI-based neuroimaging studies, it has expanded to include both general terms needed to describe experiments and studies and domain-specific terms for non-MRI data.</p> | ||
| <p>While NIDM-E should currently be considered a "terminology" it is built from collections of terms from existing ontologies and augmented only when a needed term either does not exist in an ontology or the existing term has a different meaning or usage from that relevant for NIDM-E. The basis of NIDM-E is PROV-O, an W3C provenance ontology that has as its base elements, Entities, Activities, and Agents. Other terms have been imported from general ontologies as diverse and the Semanticscience Integrated Ontology (SIO) and the Information Artifact Ontology (IAO), and from domain-specific ontologies such as Ontoneurolog. NIDM-E also contains collections of terms that are used in the Brain Imaging Data Structure (BIDS) and DICOM standards.</p> | ||
| <p>Almost all terms in NIDM-E contain either definitions, or in the case of the BIDS terms, descriptions (which are not formal definitions). There are a few exceptions from ontologies in which most imported terms have definitions, but a very few do not. Terms imported into NIDM-E keep the definition from the parent ontology. Non-imported terms, those not found in other ontologies and created specifically for NIDM-E, all have definitions in the form of "X is a Y which Zs", where X is the term, Y is the genus and Z are the differentia (Seppala, Ruttenburg, Smith. Ci.Inf., Brasília, DF, v.46 n.1, p.73-88, jan./abr. 2017).</p> | ||
| <p>The terms in NIDM-E are broken into several categories: classes, datatype properties, object properties, annotation properties, and named individuals. Terms considered to be classes are general terms that often describe what an experimental variable is "about", e.g., "age". Datatype properties connect numerical values to Entities, while object properties connect Entities and annotation properties are used to attach a note to an Entity that describes something about the Entity.</p> | ||
| <p>NIDM-E should also be considered "under construction". As noted above, the initial terms in NIDM-E were related to MRI-based neuroimaging, but NIDM-E has been constructed such that "hooks" exist that can be used to add terms needed to annotate terms from other modalities. NIDM-E was built by selecting terms needed to annotate real datasets and has expanded as new datasets are considered. As such, NIDM-E is a "practical", rather than "theoretical" terminology and so terms may be missing that may be useful, but were not needed for the datasets upon which NIDM-E was built to describe.</p> | ||
| <p>Suggestions for new terms, edits to term parentage, and term definitions are welcome. These can be suggested using the Issues function in GitHub <a href="https://github.com/incf-nidash/nidm-experiment">here</a>. Click on "Issues" -> "New issue" and a list of issue-type templates will become available. These can be used to make suggestions and track the discussion and resolution of each issue.</p> | ||
| <p>A use case for NIDM-E is shown below to illustrate how the MRI acquisition activity might be modeled.</p> | ||
| <p>This is the Term Resolution page for NIDM-Experiment Based on BFO/COB (NEC), meaning that each term in NEC has a URI that can be referred to when the term is used in a semantic web application. For example, <a href="#blooddraw">https://incf-nidash.github.io/NIDM-Experiment-COB/index.html#blooddraw</a> points to the entry on this page for the term nidm:blooddraw, in the nidm namespace.</p> | ||
| <p>NEC (NIDM-Experiment based on COB) is an effort to construct a sound ontological basis for the NIDM-Experiment ontology, by using the Basic Formal Ontology as the foundational term set. We also have leveraged and the Core Ontology for Biology and Biomedicine (COB) which has been created as a "starter set" ontology – a smaller subset of terms from BFO that adheres to the BFO organization and adds some terms commonly used in biology and biomedicine. By basing a new ontology on BFO/COB, we can leverage a wide array of ontologies such as the Ontology of Biomedical Investigations (OBI), which contains many terms useful in describing neuroscientific experiments. This means that all the data in an experiment which collects MRI, PET, CT, blood samples, and neuropsychological instrument data can be modeled by NEC to an arbitrary level of detail and within the same framework, which facilitates all the data to be Findable, Reusable, and Interoperable – part of the FAIR Principles.</p> | ||
| <p>NEC is an ontology that can be used to describe neuroscience-related experiments. While NIDM-E was initially constructed to describe MRI-based neuroimaging studies, it has since been expanded to include both general terms needed to describe experiments using other non-MRI data acquisition modalities.</p> | ||
| <p>The conversion of NIDM-E from an earlier version as a PROV-based controlled terminology to a BFO-based ontology is ongoing. It is built from collections of terms from existing BFO-related ontologies and augmented only when a needed term either does not exist in an active or recent ontology or the existing terms have a different meaning or usage from that relevant for NIDM-E. NIDM-E also contains collections of terms that are used in the Brain Imaging Data Structure (BIDS) and terms that represent the full set of DICOM tags.</p> | ||
| <p>All terms in NIDM-E contain either definition or, in the case of the BIDS terms, descriptions (which are not formal definitions). Terms imported into NIDM-E keep the definition from the parent ontology. Terms created specifically for NIDM-E, all have definitions in the form of "X is a Y which Zs", where X is the term, Y is the genus and Z are the differentia (Seppala, Ruttenburg, Smith. Ci.Inf., Brasília, DF, v.46 n.1, p.73-88, jan./abr. 2017).</p> | ||
| <p>The terms in NIDM-E are broken into several categories: classes, datatype properties, object properties, annotation properties, and named individuals. Terms considered to be classes are general terms that often describe what an experimental variable is "about", e.g., "age". Datatype properties connect numerical values to Entities, while object properties connect Entities and annotation properties are used to attach a note to an Entity that describes something about the Entity.</p> | ||
| <p>NEC should also be considered "under construction". As noted above, the initial terms in NIDM-E were related to MRI-based neuroimaging, but NIDM-E (and now NEC) has been constructed such that "hooks" exist that can be used to add terms needed to annotate terms from other modalities.</p> | ||
| <p>NIDM-E was built by selecting terms needed to annotate real datasets and has expanded as new datasets are considered. As such, NEC is a "practical", rather than "theoretical" terminology and so terms may be missing that may be useful, but were not needed for the datasets upon which NIDM-E was built to describe. Suggestions for new terms, edits to term parentage, and term definitions are welcome. These can be suggested using the Issues function in GitHub. Click on "Issues" -> "New issue" and a list of issue-type templates will become available. These can be used to make suggestions and track the discussion and resolution of each issue. We are also actively providing feedback to other ontologies on the terms we have imported in NEC.</p> | ||
| <p> | ||
| <figure id="Small_imaging_example"> | ||
| <img src="img/Small_imaging_example.png" /> | ||
| <img src="img/BFO_Small_imaging_example.png" /> | ||
| </figure> | ||
| </p> | ||
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