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1.  How the gene ontology evolves 
BMC Bioinformatics  2011;12:325.
Background
Maintaining a bio-ontology in the long term requires improving and updating its contents so that it adequately captures what is known about biological phenomena. This paper illustrates how these processes are carried out, by studying the ways in which curators at the Gene Ontology have hitherto incorporated new knowledge into their resource.
Results
Five types of circumstances are singled out as warranting changes in the ontology: (1) the emergence of anomalies within GO; (2) the extension of the scope of GO; (3) divergence in how terminology is used across user communities; (4) new discoveries that change the meaning of the terms used and their relations to each other; and (5) the extension of the range of relations used to link entities or processes described by GO terms.
Conclusion
This study illustrates the difficulties involved in applying general standards to the development of a specific ontology. Ontology curation aims to produce a faithful representation of knowledge domains as they keep developing, which requires the translation of general guidelines into specific representations of reality and an understanding of how scientific knowledge is produced and constantly updated. In this context, it is important that trained curators with technical expertise in the scientific field(s) in question are involved in supervising ontology shifts and identifying inaccuracies.
doi:10.1186/1471-2105-12-325
PMCID: PMC3166943  PMID: 21819553
Gene Ontology; knowledge; maintenance; curation; ontology shifts
2.  NeuroNames: An Ontology for the BrainInfo Portal to Neuroscience on the Web 
Neuroinformatics  2012;10(1):97-114.
BrainInfo (http://braininfo.org) is a growing portal to neuroscientific information on the Web. It is indexed by NeuroNames, an ontology designed to compensate for ambiguities in neuroanatomical nomenclature. The 20-year old ontology continues to evolve toward the ideal of recognizing all names of neuroanatomical entities and accommodating all structural concepts about which neuroscientists communicate, including multiple concepts of entities for which neuroanatomists have yet to determine the best or ‘true’ conceptualization. To make the definitions of structural concepts unambiguous and terminologically consistent we created a ‘default vocabulary’ of unique structure names selected from existing terminology. We selected standard names by criteria designed to maximize practicality for use in verbal communication as well as computerized knowledge management. The ontology of NeuroNames accommodates synonyms and homonyms of the standard terms in many languages. It defines complex structures as models composed of primary structures, which are defined in unambiguous operational terms. NeuroNames currently relates more than 16,000 names in eight languages to some 2,500 neuroanatomical concepts. The ontology is maintained in a relational database with three core tables: Names, Concepts and Models. BrainInfo uses NeuroNames to index information by structure, to interpret users’ queries and to clarify terminology on remote web pages. NeuroNames is a resource vocabulary of the NLM’s Unified Medical Language System (UMLS, 2011) and the basis for the brain regions component of NIFSTD (NeuroLex, 2011). The current version has been downloaded to hundreds of laboratories for indexing data and linking to BrainInfo, which attracts some 400 visitors/day, downloading 2,000 pages/day.
doi:10.1007/s12021-011-9128-8
PMCID: PMC3247656  PMID: 21789500
NeuroNames; BrainInfo; ontology; web portal; neuroanatomical nomenclature; web search
3.  Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies 
PLoS ONE  2014;9(3):e89606.
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
doi:10.1371/journal.pone.0089606
PMCID: PMC3940615  PMID: 24595056
4.  The Representation of Heart Development in the Gene Ontology 
Developmental Biology  2011;354(1):9-17.
An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling.
In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development and aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject.
The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area.
doi:10.1016/j.ydbio.2011.03.011
PMCID: PMC3302178  PMID: 21419760
annotation; cardiovascular; development; Gene Ontology; heart
5.  The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations 
Nucleic Acids Research  2008;36(Database issue):D449-D454.
The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.
doi:10.1093/nar/gkm908
PMCID: PMC2238838  PMID: 18194960
6.  The Gene Ontology in 2010: extensions and refinements 
Nucleic Acids Research  2009;38(Database issue):D331-D335.
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.
doi:10.1093/nar/gkp1018
PMCID: PMC2808930  PMID: 19920128
7.  Hematopoietic Cell Types: Prototype for a Revised Cell Ontology 
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. The CL is a candidate reference ontology of the OBO Foundry and requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology. We have now addressed the specific content of one area of the CL, the section of the ontology dealing with hematopoietic cells. This section has been extensively revised to improve its content and eliminate multiple inheritance in the asserted hierarchy, and the groundwork was laid for structuring the hematopoietic cell type terms as cross-products incorporating logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvements to the CL in this area represent a paradigm for improvement of the entire ontology over time.
doi:10.1016/j.jbi.2010.01.006
PMCID: PMC2892030  PMID: 20123131
ontology; hematopoietic cells; immunology
8.  The Gene Ontology (GO) project in 2006 
Nucleic Acids Research  2005;34(Database issue):D322-D326.
The Gene Ontology (GO) project () develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see ). The GO Consortium continues to improve to the vocabulary content, reflecting the impact of several novel mechanisms of incorporating community input. A growing number of model organism databases and genome annotation groups contribute annotation sets using GO terms to GO's public repository. Updates to the AmiGO browser have improved access to contributed genome annotations. As the GO project continues to grow, the use of the GO vocabularies is becoming more varied as well as more widespread. The GO project provides an ontological annotation system that enables biologists to infer knowledge from large amounts of data.
doi:10.1093/nar/gkj021
PMCID: PMC1347384  PMID: 16381878
9.  LexGrid: A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime 
Many biomedical terminologies, classifications, and ontological resources such as the NCI Thesaurus (NCIT), International Classification of Diseases (ICD), Systematized Nomenclature of Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings. However, virtually all these resources involve incompatible formats, are based on different modeling languages, and lack appropriate tooling and programming interfaces (APIs) that hinder their wide-scale adoption and usage in a variety of application contexts. The Lexical Grid (LexGrid) project introduced in this paper is an ongoing community-driven initiative, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, designed to bridge this gap using a common terminology model called the LexGrid model. The key aspect of the model is to accommodate multiple vocabulary and ontology distribution formats and support of multiple data stores for federated vocabulary distribution. The model provides a foundation for building consistent and standardized APIs to access multiple vocabularies that support lexical search queries, hierarchy navigation, and a rich set of features such as recursive subsumption (e.g., get all the children of the concept penicillin). Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services.
doi:10.1197/jamia.M3006
PMCID: PMC2732233  PMID: 19261933
10.  On gene ontology and function annotation 
Bioinformation  2006;1(3):97-98.
The effort of function annotation does not merely involve associating a gene with some structured vocabulary that describes action. Rather the details of the actions, the components of the actions, the larger context of the actions are important issues that are of direct relevance, because they help understand the biological system to which the gene/protein belongs. Currently Gene Ontology (GO) Consortium offers the most comprehensive sets of relationships to describe gene/protein activity. However, its choice to segregate gene ontology to subdomains of molecular function, biological process and cellular component is creating significant limitations in terms of future scope of use. If we are to understand biology in its total complexity, comprehensive ontologies in larger biological domains are essential. A vigorous discussion on this topic is necessary for the larger benefit of the biological community. I highlight this point because larger-bio-domain ontologies cannot be simply created by integrating subdomain ontologies. Relationships in larger bio-domain-ontologies are more complex due to larger size of the system and are therefore more labor intensive to create. The current limitations of GO will be a handicap in derivation of more complex relationships from the high throughput biology data.
PMCID: PMC1891657  PMID: 17597866
gene; ontology; function; annotation; vocabulary
11.  The Gene Ontology: enhancements for 2011 
Nucleic Acids Research  2011;40(D1):D559-D564.
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.
doi:10.1093/nar/gkr1028
PMCID: PMC3245151  PMID: 22102568
12.  The Open Biomedical Annotator 
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. This paper presents the Open Biomedical Annotator (OBA), an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata (www.bioontology.org). The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data.[1]
PMCID: PMC3041576  PMID: 21347171
13.  The Gene Ontology project in 2008 
Nucleic Acids Research  2007;36(Database issue):D440-D444.
The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of ‘reference’ genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface.
doi:10.1093/nar/gkm883
PMCID: PMC2238979  PMID: 17984083
14.  Bringing Ontology to the Gene Ontology 
We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. Making such controlled vocabularies maximally useful in support of bioinformatics applications requires explicating in machine-processible form the implicit background information that enables human users to interpret the meaning of the vocabulary terms. In the case of GO, this process would involve rendering the meanings of GO into a formal (logical) language with the help of domain experts, and adding additional information required to support the chosen formalization. A controlled vocabulary augmented in these ways is commonly called an ontology. In this paper, we make a modest exploration to determine the ontological requirements for this extended version of GO. Using the terms within the three GO hierarchies (molecular function, biological process and cellular component), we investigate the facility with which GO concepts can be ontologized, using available tools from the philosophical and ontological engineering literature.
doi:10.1002/cfg.253
PMCID: PMC2447385  PMID: 18629099
15.  The Plant Ontology™ Consortium and Plant Ontologies 
The goal of the Plant Ontology™ Consortium is to produce structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology of the relevant plant taxa (e.g. development, anatomy, morphology, genomics, proteomics) is accumulating and changing. The collaborators of the Plant Ontology™ Consortium (POC) represent a number of core participant database groups. The Plant Ontology™ Consortium is expanding the paradigm of the Gene Ontology™ Consortium (http://www.geneontology.org). Various trait ontologies (agronomic traits, mutant phenotypes, phenotypes, traits, and QTL) and plant ontologies (plant development, anatomy [incl. morphology]) for several taxa (Arabidopsis, maize/corn/Zea mays and rice/Oryza) are under development. The products of the Plant Ontology™ Consortium will be open-source.
doi:10.1002/cfg.154
PMCID: PMC2447263  PMID: 18628842
16.  How to link ontologies and protein–protein interactions to literature: text-mining approaches and the BioCreative experience 
There is an increasing interest in developing ontologies and controlled vocabularies to improve the efficiency and consistency of manual literature curation, to enable more formal biocuration workflow results and ultimately to improve analysis of biological data. Two ontologies that have been successfully used for this purpose are the Gene Ontology (GO) for annotating aspects of gene products and the Molecular Interaction ontology (PSI-MI) used by databases that archive protein–protein interactions. The examination of protein interactions has proven to be extremely promising for the understanding of cellular processes. Manual mapping of information from the biomedical literature to bio-ontology terms is one of the most challenging components in the curation pipeline. It requires that expert curators interpret the natural language descriptions contained in articles and infer their semantic equivalents in the ontology (controlled vocabulary). Since manual curation is a time-consuming process, there is strong motivation to implement text-mining techniques to automatically extract annotations from free text. A range of text mining strategies has been devised to assist in the automated extraction of biological data. These strategies either recognize technical terms used recurrently in the literature and propose them as candidates for inclusion in ontologies, or retrieve passages that serve as evidential support for annotating an ontology term, e.g. from the PSI-MI or GO controlled vocabularies. Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information Extraction Systems in Biology) challenge. Special emphasis is given to protein–protein interaction data and PSI-MI terms referring to interaction detection methods.
doi:10.1093/database/bas017
PMCID: PMC3309177  PMID: 22438567
17.  A Unified Anatomy Ontology of the Vertebrate Skeletal System 
PLoS ONE  2012;7(12):e51070.
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.
doi:10.1371/journal.pone.0051070
PMCID: PMC3519498  PMID: 23251424
18.  The @neurIST Ontology of Intracranial Aneurysms: Providing Terminological Services for an Integrated IT Infrastructure 
The @neurIST ontology is currently under development within the scope of the European project @neurIST intended to serve as a module in a complex architecture aiming at providing a better understanding and management of intracranial aneurysms and subarachnoid hemorrhages. Due to the integrative structure of the project the ontology needs to represent entities from various disciplines on a large spatial and temporal scale. Initial term acquisition was performed by exploiting a database scaffold, literature analysis and communications with domain experts. The ontology design is based on the DOLCE upper ontology and other existing domain ontologies were linked or partly included whenever appropriate (e.g., the FMA for anatomical entities and the UMLS for definitions and lexical information). About 2300 predominantly medical entities were represented but also a multitude of biomolecular, epidemiological, and hemodynamic entities. The usage of the ontology in the project comprises terminological control, text mining, annotation, and data mediation.
PMCID: PMC2655878  PMID: 18693797
Medical Informatics Applications; Ontology design; Intracranial aneurysm; Subarachnoid hemorrhage; Terminology
19.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration 
Nature biotechnology  2007;25(11):1251.
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.
doi:10.1038/nbt1346
PMCID: PMC2814061  PMID: 17989687
20.  Foundations for a realist ontology of mental disease 
While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient.
We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology (BFO) and in the application of BFO in the Ontology of General Medical Science (OGMS). We analyzed statements about what counts as a mental disease provided (1) in the research agenda for the DSM-V, and (2) in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions.
Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future.
doi:10.1186/2041-1480-1-10
PMCID: PMC3017014  PMID: 21143905
21.  Concept annotation in the CRAFT corpus 
BMC Bioinformatics  2012;13:161.
Background
Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.
Results
This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement.
Conclusions
As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.
doi:10.1186/1471-2105-13-161
PMCID: PMC3476437  PMID: 22776079
22.  Gene Ontology Annotations and Resources 
Nucleic Acids Research  2012;41(D1):D530-D535.
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
doi:10.1093/nar/gks1050
PMCID: PMC3531070  PMID: 23161678
23.  PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies 
With the emergence of tools for collaborative ontology engineering, more and more data about the creation process behind collaborative construction of ontologies is becoming available. Today, collaborative ontology engineering tools such as Collaborative Protégé offer rich and structured logs of changes, thereby opening up new challenges and opportunities to study and analyze the creation of collaboratively constructed ontologies. While there exists a plethora of visualization tools for ontologies, they have primarily been built to visualize aspects of the final product (the ontology) and not the collaborative processes behind construction (e.g. the changes made by contributors over time). To the best of our knowledge, there exists no ontology visualization tool today that focuses primarily on visualizing the history behind collaboratively constructed ontologies. Since the ontology engineering processes can influence the quality of the final ontology, we believe that visualizing process data represents an important stepping-stone towards better understanding of managing the collaborative construction of ontologies in the future. In this application paper, we present a tool – PragmatiX – which taps into structured change logs provided by tools such as Collaborative Protégé to visualize various pragmatic aspects of collaborative ontology engineering. The tool is aimed at managers and leaders of collaborative ontology engineering projects to help them in monitoring progress, in exploring issues and problems, and in tracking quality-related issues such as overrides and coordination among contributors. The paper makes the following contributions: (i) we present PragmatiX, a tool for visualizing the creation process behind collaboratively constructed ontologies (ii) we illustrate the functionality and generality of the tool by applying it to structured logs of changes of two large collaborative ontology-engineering projects and (iii) we conduct a heuristic evaluation of the tool with domain experts to uncover early design challenges and opportunities for improvement. Finally, we hope that this work sparks a new line of research on visualization tools for collaborative ontology engineering projects.
doi:10.4018/jswis.2013010103
PMCID: PMC3901413  PMID: 24465189
Collaborative Ontology Engineering; pragmatic analysis; ontology monitoring; ontology engineering visualization; ontology evaluation; ontology tool
24.  Mapping the Gene Ontology Into the Unified Medical Language System 
We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions between the UMLS and GO teams, the GO was integrated with the UMLS. Overall, a total of 23% of the GO terms either matched directly (3%) or linked (20%) to existing UMLS concepts. All GO terms now have a corresponding, official UMLS concept, and the entire vocabulary is available through the web-based UMLS Knowledge Source Server. The mapping of the Gene Ontology, with its focus on structures, processes and functions at the molecular level, to the existing broad coverage UMLS should contribute to linking the language and practices of clinical medicine to the language and practices of genomics.
doi:10.1002/cfg.407
PMCID: PMC2447454  PMID: 18629164
25.  DeMO: An Ontology for Discrete-event Modeling and Simulation 
Simulation  2011;87(9):747-773.
Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community.
doi:10.1177/0037549710386843
PMCID: PMC3423901  PMID: 22919114
Discrete systems; simulation environments; standards; Web-based environments

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