Terminology and Language Issues

Terminology Problems

In different models of the same species, parts with similar names may only denote roughly the same tissues.
In GALEN:     Lobe of left lung

Maps in FMA to:     Upper Lobe of left lung
Lower lobe of left lung

More of a problem is that in anatomical models of different species, parts with the same (or similar) names do not always denote homologous tissues:
In Mouse “tail”
(posterior extension of the spine)

In C.Elegans “tail”
(male sex organ)

The model species we are comparing have many anatomical parts. For
example, Mouse has 3559 anatomical parts, Drosophila has 506
anatomical parts, and C. Elegans, 242 anatomical parts.

Does the language used in terminologies and anatomical ontologies suggest what parts may be similar? Yes. But not directly – context is crucial. The entire series of names from root to leaf node is needed to ground terms that are themselves underspecified. Grounding refers to connecting natural language expressions such as mouse tail, with a model of the world. In this case, the model is a mouse ontology.

Context is the key to clarifying terms such as “tail”. If you look at the paths for tail in Mouse and C.Elegans, its clear that they are different:
Path name in Mouse:
embryo
tail
nervous system
peripheral nervous system
segmental spinal nerve

Path name in C.Elegans:
organ_system
sex-associated system
male-associated system
male tail
hypodermis
fan hypodermis

Language processing techniques are used to help compare anatomical part names across species. They include:

a.     Normalizing terms to limit the effect of different descriptive styles.
b.     Comparing content words by removing stop words.
c.     Ensuring comparable forms of words by stemming and lemmatizing.
d.     Results are then treated as an unordered set.

The results of the language processing experiments show that the lexical suggestions were indicative of structural support in 75% of the comparisons.

Researchers at Heriot-Watt University and the University of Edinburgh have been collaborating on projects relating to an on-line anatomy and genomic databases for a number of years. This record of collaboration was an important factor in obtaining funding for this joint project from the BBSRC.

The XSPAN project aims to support cross-species access to tissue-based genomic information through the development of an internet based cross-species anatomy network.

An ontolgy browser, COBrA has been developed and used to author mappings which are then uploaded to the XSPAN server.

The network provides interoperability between anatomy databases of the key model embryos, which will, in turn, facilitate access to gene expression and other tissue-based data across species, and to other genomics and proteomics resources.

The overall objective of XSPAN is to support cross-species access to tissue-based genetic information through the development of an internet-based cross-species anatomy network, i.e. a cross-species anatomy ontology integration system.

This system will provide interoperability between databases of key model embryos which will, in turn, facilitate access to gene expression and other tissue-based data across species, and to other genomics and proteomics resources.

XSPAN is a joint project between the School of Mathematical and Computer Sciences at Heriot-Watt University, and the Schools of Biomedical Sciences and Informatics at the University of Edinburgh.

XSPAN is funded by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC)

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