Controlled vocabulary

XML specifies the syntax of a language but not the semantics. Ontologies or other forms of controlled vocabularies or glossaries are necessary to impose semantics on an XML-based language. For example, the Semantic Web developers have proposed several languages to express the structure and relationships of data on the WWW [13]. 

The GO (Gene Ontology) project provides a controlled vocabulary to describe gene and gene product attributes in any organism. Annotated are the biological process, the molecular function, and the cellular component of gene products. 

Another POLIDCASYR extension ensures that structural features of the backbone can be distinguished from those occurring in side chains. The system furthermore augments structure codes for polymers using a controlled vocabulary of keywords, such as epoxy resin , aminoplast or phenoplast . 

In addition to fragment and graph indexing of polymer information, the POLID-CAS YR system also makes use of two distinct vocabularies for non-structural terms. The first vocabulary is, in essence, a controlled vocabulary of hierarchically ordered terms (taxonomy), supplemented by a second, more fluid vocabulary, which is subject to constant editing. The latter is used to further enhance the controlled vocabulary, e.g., the term isomerization , which is part of the controlled vocabulary, could be defined further by the terms racemization , tautomerization or rotation isomerization . Annotation of this kind is only a short step away from techniques, which we now associate with the terms tagging and folksonomies and which are typical components of Web 2.0 systems. POLIDCASYR s controlled vocabulary is structured according to a number of semantic categories such... 

Fig. 5 Subdivision of semantic categories in the POLIDCASYR controlled vocabulary...

Personal computers have introduced new ways to handle private bibliographic and text files. The most important factors to consider to achieve satisfactory results in building a bibliographic or text database are the (ype of information to be stored and Ihc needs of the user. Types of information include correspondence, research results and documentation, meeting notes, and bibliographic references. Needs of the user to be considered should include the potential number of users of the dalabase. restrictions tor the access and display of the information because of privacy or proprietary reasons, and the retrieval mechanisms (e g., by keyword, authority list, controlled vocabulary, author, title, date, or other document or information attributes). In addition, criteria for selecting and encoding information for the dalabase need to be established. 

MEDLINE (MEDlars on-LINE), NLM s on-line data base on the medical literature of the world, indexes its entries by use of MESH (MEdical Subject Heading) terms, which is a controlled vocabulary. When searching on-line, terms entered default to the MESH heading index unless a modifier specifies that another index is searched. The following MESH headings are useful for finding teratology information on MEDLINE ... 

This section will discuss the standards for sharing and discussing microarray experiments, including the ontologies and controlled vocabularies. A non-technical description of the sharing process will be provided, as well as an introduction to the pharmacology/toxicology focused version of the MIAME standard, MIAME/Tox, which is currently under development. 

The MAGE has built within it a controlled vocabulary that is used to standardize communication between data providers. However, MAGE can also be extended to encode other types of omic data beyond genomics, such as proteomic data, so long as a reference to the ontology or controlled vocabulary is provided. Although a description of the extension mechanism is beyond scope of this book, practitioners must become familiar with it in order to ensure their software products and applications will be able to accept any and all annotation data that may be submitted with the genomic data. 

To assist investigators in meeting the requirements of the standard, the MGED Society provides a MIAME-checklist. The checklist outlines the most pertinent points of the standard to facilitate data submission compliance (www.mged.org/Workgroups/MIAME/miame.html). The MIAME standard includes a glossary of the controlled vocabulary used throughout the MIAME document to assist data for submission. 

Validation guarantees that the datument conforms to rules. The more powerful the rules, the more invalid data can be detected. Thus, schemas can allow the detection of some disallowed data, particularly with a controlled vocabulary. An atom in CML is not allowed an elementType of CO (arising perhaps as a mis-... 

Many elements of a controlled vocabulary are effectively defined by software implementation. Thus, the description of the HTML language requires certain elements to have specified behavior. For example, supports the display of raster images, but the precise look may vary between implementations and file types. Implementation through software is useful and powerful where authors, publishers, readers, and processors all use the same system. Because STM publishing is increasingly multidisciplinary, this implementation becomes problematic. Often a reader may have to download specialist software that is idiosyncratic and that may not have enough functionality, especially the export of semantically rich data. Moreover, the semantic rules are often buried deep in the software and difficult to understand precisely. 

ThermoML (Frenkel et al. 2006) is a language for the storage and exchange of experimental, predicted, and critically evaluated thermophysical and thermochemical property data. The language aims to cover essentially all relevant properties, and it deals thoroughly with uncertainties (Chirico et al. 2003). The standard, which has been developed as an IUPAC project (2002-055-3-024) and become an IUPAC recommendation (Frenkel et al 2006), provides detailed controlled vocabulary for the field. Several high-profile journals already provide data in this format (http //trc. nist.gov/ThermoML.html), and if this trend continues in the future, introduction of ThermoML may be rightfully considered as one of the milestone achievements in the rich history of thermodynamics research. 

Nomenclatures, terminologies, and controlled vocabularies established in molecular biology, for example, GO, are a basis for NER, but when mining literature, we always have to keep in mind that the use of terms describing the functions of proteins took place before GO was established, and the meaning of certain functional descriptions might have changed over time.32... 

At an initial HUPO-PSI-sponsored meeting of this group it was decided that the approach to designing such a format should be multilayered, with Level 1 designed to fulfil basic requirements and be suitable for rapid implementahon. Subsequent levels will supply further complexity and flexibility, for example the ability to deal with other interactors such as nucleic acids. Wherever possible, the potential values of attributes in the data model are defined by controlled vocabularies researchers may also ascribe confidence levels to the data at various points throughout the data entry process and add free comments in appropriate places. 

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