The ontology of craniofacial development and malformation for translational craniofacial research.

We introduce the Ontology of Craniofacial Development and Malformation (OCDM) as a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to facilitate integrating craniofacial data obtained via multiple techniques from multiple labs and at multiple levels of granularity. The OCDM is a project of the NIDCR-sponsored FaceBase Consortium, whose goal is to promote and enable research into the genetic and epigenetic causes of specific craniofacial abnormalities through the provision of publicly accessible, integrated craniofacial data. However, the OCDM should be usable for integrating any web-accessible craniofacial data, not just those data available through FaceBase. The OCDM is based on the Foundational Model of Anatomy (FMA), our comprehensive ontology of canonical human adult anatomy, and includes modules to represent adult and developmental craniofacial anatomy in both human and mouse, mappings between homologous structures in human and mouse, and associated malformations. We describe these modules, as well as prototype uses of the OCDM for integrating craniofacial data. By using the terms from the OCDM to annotate data, and by combining queries over the ontology with those over annotated data, it becomes possible to create "intelligent" queries that can, for example, find gene expression data obtained from mouse structures that are precursors to homologous human structures involved in malformations such as cleft lip. We suggest that the OCDM can be useful not only for integrating craniofacial data, but also for expressing new knowledge gained from analyzing the integrated data.

Spatial-symbolic Query Engine in Anatomy.

OBJECTIVES: Currently, the primary means for answering anatomical questions such as 'what vital organs would potentially be impacted by a bullet wound to the abdomen?' is to look them up in textbooks or to browse online sources. In this work we describe a semantic web service and spatial query processor that permits a user to graphically pose such questions as joined queries over separately defined spatial and symbolic knowledge sources. METHODS: Spatial relations (e.g. anterior) were defined by two anatomy experts, and based on a 3-D volume of labeled images of the thorax, all the labeled anatomical structures were queried to retrieve the target structures for every query structure and every spatial relation. A web user interface and a web service were designed to relate existing symbolic information from the Foundational Model of Anatomy ontology (FMA) with spatial information provided by the spatial query processor, and to permit users to select anatomical structures and define queries. RESULTS: We evaluated the accuracy of results returned by the queries, and since there is no independent gold standard, we used two anatomy experts' opinions as the gold standard for comparison. We asked the same experts to define the gold standard and to define the spatial relations. The F-measure for the overall evaluation is 0.90 for rater 1 and 0.56 for rater 2. The percentage of observed agreement is 99% and Cohen's kappa coefficient reaches 0.51. The main source of disagreement relates to issues with the labels used in the dataset, and not with the tool itself. CONCLUSIONS: In its current state the system can be used as an end-user application but it is likely to be of most use as a framework for building end-user applications such as displaying the results as a 3-D anatomical scene. The system promises potential practical utility for obtaining and navigating spatial and symbolic data.

The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions.

We describe the foundational model of anatomy (FMA), reference ontology for the discipline of human anatomy. Using the semantic structure of the FMA as knowledge representation template, we propose a physiology reference ontology (PRO) as a corresponding ontology for "functional bioinformatics". We envision the PRO as a source vocabulary for building symbolic representations of human physiological states and actions that may ultimately be extensible to other species. We describe the evolving architecture of the PRO, in terms of simple examples based on the anatomical concepts encoded in the FMA.

Foundational model of neuroanatomy: implications for the Human Brain Project.

In order to meet the need for a controlled terminology in neuroinformatics, we have integrated the extensive terminology of NeuroNames into the Foundational Model of anatomy. We illustrate the application of foundational principles for the establishment of an inheritance hierarchy, which accommodates anatomical attributes of neuroanatomical concepts and provides the foundation to which other information may be linked.

The role of definitions in biomedical concept representation.

The Foundational Model (FM) of anatomy, developed as an anatomical enhancement of UMLS, classifies anatomical entities in a structural context. Explicit definitions have played a critical role in the establishment of FM classes. Essential structural properties that distinguish a group of anatomical entities serve as the differentiate for defining classes. These, as well as other structural attributes, are introduced as template slots in Protégé, a frame-based knowledge acquisition system, and are inherited by descendants of the class. A set of desiderata has evolved during the instantiation of the FM for formulating definitions. We contend that 1. these desiderata generalize to non-anatomical domains and 2. satisfying them in constituent vocabularies of UMLS would enhance the quality of information retrievable through UMLS.

Influence of the Digital Anatomist Foundational Model on traditional representations of anatomical concepts.

A principled and logical representation of the structure of the human body has led to conflicts with traditional representations of the same knowledge by anatomy textbooks. The examples which illustrate resolution of these conflicts suggest that stricter requirements must be met for semantic consistency, expressivity and specificity by knowledge sources intended to support inference than by textbooks and term lists. These next-generation resources should influence traditional concept representation, rather than be constrained by convention.

Conceptualization of anatomical spatial entities in the Digital Anatomist Foundational Model.

Anatomical spatial concepts are indispensable in educational and clinical discourse, yet a system for representing these concepts has not been proposed. Guided by explicit principles and definitions of the Digital Anatomist Foundational Model, we developed an ontology of spaces, surfaces, lines and points that are associated with anatomical structures. Ontologies for Anatomical Structure and Anatomical Spatial Entity were instantiated for the thorax, abdomen, pelvis and perineum. Representing the concepts in--part of--hierarchies as well, provided formative evaluation of the classification. We invite empirical evaluation of the Foundational Model through its use for educational and clinical applications.

Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base.

OBJECTIVE: Conceptualization of the physical objects and spaces that constitute the human body at the macroscopic level of organization, specified as a machine-parseable ontology that, in its human-readable form, is comprehensible to both expert and novice users of anatomical information. DESIGN: Conceived as an anatomical enhancement of the UMLS Semantic Network and Metathesaurus, the anatomical ontology was formulated by specifying defining attributes and differentia for classes and subclasses of physical anatomical entities based on their partitive and spatial relationships. The validity of the classification was assessed by instantiating the ontology for the thorax. Several transitive relationships were used for symbolically modeling aspects of the physical organization of the thorax. RESULTS: By declaring Organ as the macroscopic organizational unit of the body, and defining the entities that constitute organs and higher level entities constituted by organs, all anatomical entities could be assigned to one of three top level classes (Anatomical structure, Anatomical spatial entity and Body substance). The ontology accommodates both the systemic and regional (topographical) views of anatomy, as well as diverse clinical naming conventions of anatomical entities. CONCLUSIONS: The ontology formulated for the thorax is extendible to microscopic and cellular levels, as well as to other body parts, in that its classes subsume essentially all anatomical entities that constitute the body. Explicit definitions of these entities and their relationships provide the first requirement for standards in anatomical concept representation. Conceived from an anatomical viewpoint, the ontology can be generalized and mapped to other biomedical domains and problem solving tasks that require anatomical knowledge.

The potential of the digital anatomist foundational model for assuring consistency in UMLS sources.

Inconsistent anatomical concept representation can be identified in anatomy textbooks and hard copy term lists, as well as in UMLS source vocabularies and other controlled medical terminologies. In this report we select some examples of inconsistent representations of anatomical concepts, and illustrate how these inconsistencies can be explained and reconciled by the Digital Anatomist Foundational Model. We use this process for gaining a measure of the validity of the logic-based Model.

The role of hematogenous and intrinsic precursor cells in lymphocyte production in murine bone marrow and thymus.

It is well recognized that the bone marrow contains cells that can repopulate a depleted thymus as well as cells that can be induced to express phenotypic markers characteristic of T cells. It is not known, however, to what extent thymocytopoiesis in the normal thymus relies on immigrant, bone marrow-derived cells, nor whether some T cell precursors have entered the bone marrow from the circulation. We used the parabiotic system to test whether thymocytopoiesis relies on progenitors intrinsic to the thymus or on cells that enter the organ from the circulation. In the same system, we have also investigated whether Thy-1- bone marrow lymphocytes that respond to phytohemagglutinin (PHA) by proliferation and Thy-1 expression are produced by myelogenous or hematogenous progenitors. Syngeneic CBA/HT6 and CBA/CaJ mice were joined in parabiotic union at 4-6 weeks of age. Cross circulation between the two partners was verified by the equilibration of Evans' blue dye injected into one partner and by the equilibration of PHA-responsive T cells in the spleen of the parabionts. Chromosome spreads were prepared from the PHA-stimulated T cell-depleted bone marrow and from spontaneously proliferating thymocytes as well as from thymocytes stimulated by PHA or Concanavalin A (Con A). The exchange of spleen colony-forming units (CFU-S) in the femoral marrow was assessed by karyotyping individual spleen colonies. Regardless of the length of parabiotic union, ranging from 4 to 20 weeks, Thy-1-, PHA-responsive bond marrow lymphocytes remained predominantly of the host type with only 3% being derived from the opposite partner.(ABSTRACT TRUNCATED AT 250 WORDS)

Selective binding of Dolichos biflorus agglutinin to L3T4-, Lyt-2- thymocytes. Expression of terminal alpha-linked N-acetyl-D-galactosamine residues defines a subpopulation of fetal and adult murine thymocytes.

Using histochemical and immunocytochemical techniques, a lectin with nominal specificity for alpha-linked N-acetyl-D-galactosamine, Dolichos biflorus agglutinin (DBA), was found to preferentially label thymocytes with an L3T4-, Lyt-2- phenotype from fetal/newborn and adult mice. Through days 14 to 16 of gestation, virtually all thymocytes bound DBA, followed by a dramatic reduction of DBA labeling during the last 4 days of gestation, reaching adult levels of about 2 to 4% of total thymocytes. At later stages of fetal development, the DBA+ cells were confined to the subcapsular area of the thymus. This apparent loss of DBA+ cells was caused by an expansion of the thymocyte population not labeled with this lectin. Affinity purification of thymocyte cell surface components with insolubilized DBA indicated that virtually all of the lectin binding to fetal thymocytes was mediated by a 120-kDa glycoprotein. In addition to thymocytes, DBA also labeled about 5% of bone marrow cells from both normal or nude mice and a small population of spleen cells as well. These results suggest that this lectin may be useful to positively select for LT34-, Lyt-2- thymocytes, and, possibly, other immature populations within the T cell lineage.