Controlled vocabularies in bioinformatics: a case study in the gene ontology

Purpose – The purpose of this article is to evaluate the development and use of the gene ontology (GO), a scientific vocabulary widely used in molecular biology databases, with particular reference to the relation between the theoretical basis of the GO, and the pragmatics of its application. Design/methodology/approach – The study uses a combination of bibliometric analysis, content analysis and discourse analysis. These analyses focus on details of the ways in which the terms of the ontology are amended and deleted, and in which they are applied by users. Findings – Although the GO is explicitly based on an objective realist epistemology, a considerable extent of subjectivity and social factors are evident in its development and use. It is concluded that bio-ontologies could beneficially be extended to be pluralist, while remaining objective, taking a view of concepts closer to that of more traditional controlled vocabularies. Originality/value – This is one of very few studies which evaluate the development of a formal ontology in relation to its conceptual foundations, and the first to consider the GO in this way.

Download Full-text

Record linking in the EHRI portal

Records Management Journal ◽

10.1108/rmj-08-2019-0045 ◽

2020 ◽

Vol 30 (3) ◽

pp. 363-378

Author(s):

Sigal Arie Erez ◽

Tobias Blanke ◽

Mike Bryant ◽

Kepa Rodriguez ◽

Reto Speck ◽

...

Keyword(s):

Design Methodology ◽

Open Data ◽

Controlled Vocabularies ◽

Content Type ◽

Domain Specific ◽

Historical Archives ◽

Finding Aids ◽

Rich Data ◽

Significant Attention

Purpose This paper aims to describe the European Holocaust Research Infrastructure (EHRI) project's ongoing efforts to virtually integrate trans-national archival sources via the reconstruction of collection provenance as it relates to copy collections (material copied from one archive to another) and the co-referencing of subject and authority terms across material held by distinct institutions. Design/methodology/approach This paper is a case study of approximately 6,000 words length. The authors describe the scope of the problem of archival fragmentation from both cultural and technical perspectives, with particular focus on Holocaust-related material, and describe, with graph-based visualisations, two ways in which EHRI seeks to better integrate information about fragmented material. Findings As a case study, the principal contributions of this paper include reports on our experience with extracting provenance-based connections between archival descriptions from encoded finding aids and the challenges of co-referencing access points in the absence of domain-specific controlled vocabularies. Originality/value Record linking in general is an important technique in computational approaches to humanities research and one that has rightly received significant attention from scholars. In the context of historical archives, however, the material itself is in most cases not digitised, meaning that computational attempts at linking must rely on finding aids which constitute much fewer rich data sources. The EHRI project’s work in this area is therefore quite pioneering and has implications for archival integration on a larger scale, where the disruptive potential of Linked Open Data is most obvious.

Download Full-text

Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: Three tool comparison

Computers in Biology and Medicine ◽

10.1016/j.compbiomed.2005.04.008 ◽

2006 ◽

Vol 36 (7-8) ◽

pp. 731-747 ◽

Cited By ~ 8

Author(s):

Marco Masseroli ◽

Francesco Pinciroli

Keyword(s):

Gene Ontology ◽

High Throughput ◽

Controlled Vocabularies

Download Full-text

Empowering the access to public procurement opportunities by means of linking controlled vocabularies. A case study of Product Scheme Classifications in the European e-Procurement sector

Computers in Human Behavior ◽

10.1016/j.chb.2013.07.046 ◽

2014 ◽

Vol 30 ◽

pp. 674-688 ◽

Cited By ~ 7

Author(s):

Jose María Alvarez-Rodríguez ◽

José Emilio Labra-Gayo ◽

Alejandro Rodríguez-González ◽

Patricia Ordoñez De Pablos

Keyword(s):

Public Procurement ◽

Controlled Vocabularies

Download Full-text

Mining Gene Ontology Data with AGENDA

Bioinformatics and Biology Insights ◽

10.4137/bbi.s9101 ◽

2012 ◽

Vol 6 ◽

pp. BBI.S9101

Author(s):

Guvanch Ovezmyradov ◽

Qianhao Lu ◽

Martin C. Göpfert

Keyword(s):

Gene Ontology ◽

Open Source ◽

Genetic Information ◽

Collaborative Effort ◽

Controlled Vocabularies ◽

Web Based ◽

Commercial Use ◽

Diverse Species ◽

Go Terms ◽

The Web

The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-based application that is freely available for non-commercial use at the project homepage. URL: http://sourceforge.net/projects/bioagenda .

Download Full-text

A Pipeline for Non-model Organisms for de novo Transcriptome Assembly, Annotation, and Gene Ontology Analysis Using Open Tools: Case Study with Scots Pine

BIO-PROTOCOL ◽

10.21769/bioprotoc.3912 ◽

2021 ◽

Vol 11 (3) ◽

Author(s):

Gustavo Duarte ◽

Polina Yu. ◽

Stanislav Geras’kin

Keyword(s):

Gene Ontology ◽

Scots Pine ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

Gene Ontology Analysis ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome

Download Full-text

The access(ibility) of films in artist-run centres

10.32920/ryerson.14647242 ◽

2021 ◽

Author(s):

Deidre Simmons

Keyword(s):

Real Time ◽

Current Literature ◽

Social Tagging ◽

Retrieval Process ◽

Controlled Vocabularies ◽

Distribution Centre ◽

Search And Retrieval

This thesis considers how artist-run centres are creating access to their film collections by using the Canadian Filmmakers Distribution Centre (CFMDC) as its case study. It looks at current literature on accessibility, including controlled vocabularies, keywords, folksonomies, and social tagging, and how two other institutions- Institut National de l’Audiovisuel (INA), located in Paris, France and IsumaTV, located in Igloolik, Nunavut, Canada- are currently creating access to their film collections to discover how different forms of accessibility are being used in real time. It looks at how the CFMDC is currently creating access to its film collection and finally, recommends the ways accessibility at an artist-run centre could be improved to help the artist-run centre reach a wider audience, help the researcher in the search and retrieval process, and to keep the film object itself accessible.

Download Full-text