By Albert Burger, Duncan Davidson, Richard Baldock
This publication presents a well timed and first-of-its-kind number of papers on anatomy ontologies. it's interdisciplinary in its process, bringing jointly the appropriate services from computing and biomedical reviews. The booklet goals to supply readers with a accomplished knowing of the rules of anatomical ontologies and the-state-of-the-art by way of current instruments and purposes. It additionally highlights demanding situations that stay this present day.
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Extra info for Anatomy Ontologies for Bioinformatics: Principles and Practice (Computational Biology)
Example text
In addition, and perhaps more important, far better visual support than is currently available is needed for viewing subdomains of ontologies so that that anatomical knowledge can be made more accessible to the wider community. Thus far, OBOedit provides a graphical DAG which shows all the relationships associated with a concept. The Prot´eg´e environment has a graphical plug-in. COBrA just provide parent and children data as text, but a graphical viewer is under construction. As ontologies become richer, so the information becomes more complex and harder for the user to appreciate.
The term whole plant was also introduced at the top level of the PSO (it was previously used in annotations by the three databases). This term is not a botanical term and is intentionally left without children terms. Thus, we recommend that the term whole plant is used as a last option, only when precise annotation to any other term in the PO is not possible. Plant cell types are included in the PSO, but subcellular structures are not, since GO describes these in the cellular component ontology.
Non-botanical and crop-specific agronomical terms would be avoided as much as possible. 3. Terms describing developmental stages would be excluded from the PSO. 4. Attributes of terms would be avoided. 5. Most importantly, synonymy would be used whenever possible, to group speciesspecific terms. We also established criteria of what would constitute a valid term in PSO. Terms in PSO are morphological and anatomical structures of a flowering plant, from a cell to the whole plant level. Unlike in botanical or taxonomical glossaries, descriptors (also called attributes or qualifiers) are intentionally omitted.