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WormBase 2014: new views of curated biology

Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian Grove, Kevin Howe, Ranjana Kishore, Raymond Lee (+21 others)
2013 Nucleic Acids Research  
BIOLOGICAL TOPICS CURATION For 13 years, WormBase curators have been collecting data of various types pertaining to the biology of C. elegans and related nematodes.  ...  When launched, WormBase expanded prior community-driven curation to touch on virtually every aspect of classical and modern experimental biology, including next-generation sequence and high-throughput  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1063 pmid:24194605 pmcid:PMC3965043 fatcat:lh2mkgbydvfwrdngdv7nz3icme

The GOA database: Gene Ontology annotation updates for 2015

Rachael P. Huntley, Tony Sawford, Prudence Mutowo-Meullenet, Aleksandra Shypitsyna, Carlos Bonilla, Maria J. Martin, Claire O'Donovan
2014 Nucleic Acids Research  
Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups.  ...  functional information to proteins from a wide range of species.  ...  ACKNOWLEDGEMENTS GOA would like to thank curators from the UniProt Consortium and the GO Consortium, and all groups who contribute GO annotations for inclusion into our database. FUNDING  ... 
doi:10.1093/nar/gku1113 pmid:25378336 pmcid:PMC4383930 fatcat:i5ngdmj67fbxtpnkuqbo7kuwum

Exploring the Development and Maintenance Practices in the Gene Ontology

Shuheng Wu, Besiki Stvilia
2014 Advances in Classification Research Online  
The Gene Ontology (GO) is one of the most widely used and successful bio-ontologies in biomedicine and molecular biology.  ...  Guided by Activity Theory and a theoretical Information Quality Assessment Framework, this study conducts qualitative content analysis of GO's curation discussions.  ...  The findings showed that GO users and curators use QuickGO to generate graph views of a subset of GO to facilitate their quality discussions and negotiations.  ... 
doi:10.7152/acro.v24i1.14675 fatcat:w7yq5zxnb5hlrbsxrrtuqvlzd4

The BioGRID interaction database: 2015 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon (+10 others)
2014 Nucleic Acids Research  
As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms.  ...  In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove and Paul Sternberg at WormBase for ongoing collaborative development of the Genetic Interaction Ontology. We also thank Mike Cherry  ... 
doi:10.1093/nar/gku1204 pmid:25428363 pmcid:PMC4383984 fatcat:jeok6meldzhmphu3mpxqxpeoiy

What difference does quantity make? On the epistemology of Big Data in biology

S Leonelli
2014 Big Data & Society  
of adequate curation for the vast majority of data in the life sciences.  ...  Is big data science a whole new way of doing research? And what difference does data quantity make to knowledge production strategies and their outputs?  ...  2014 enabled me to complete this manuscript; and to Brian Rappert for insightful comments on the manuscript.  ... 
doi:10.1177/2053951714534395 pmid:25729586 pmcid:PMC4340542 fatcat:x22votw2hzdzfbj3hlsvr7cuwq

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network

Sohyun Hwang, Eiru Kim, Sunmo Yang, Edward M. Marcotte, Insuk Lee
2014 Nucleic Acids Research  
Accessible bioinformatics tools will therefore facilitate translation of discoveries from model organisms into human disease biology.  ...  Much of the known gene-to-phenotype association information is distributed across diverse databases, growing rapidly due to new experimental techniques.  ...  To construct validation sets of gene-disease relationships, we downloaded 149 and 88 manually curated gene-OMIM sets from Wormbase (14) and Mouse Genome Informatics (34) , respectively, on 14 April  ... 
doi:10.1093/nar/gku434 pmid:24861622 pmcid:PMC4086117 fatcat:yocggs6rojeczjhjbcrgjhydve

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
2019 F1000Research  
The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery.  ...  This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them  ...  Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience  ... 
doi:10.12688/f1000research.18238.1 fatcat:mdt6bijqlveanplh4bmca5towu

Data publication consensus and controversies

John Kratz, Carly Strasser
2014 F1000Research  
Here, we present an overview of data publication initiatives underway and the current conversation, highlighting points of consensus and issues still in contention.  ...  "Ocean Biodiversity Informatics" enabling a new era in marine biology research and management. 316, 203-214.  ...  Every two months, WormBase administrators respond to new data and better computational models by issuing a revised version with new material added and inaccurate material deleted or corrected.  ... 
doi:10.12688/f1000research.3979.1 pmid:25075301 pmcid:PMC4097345 fatcat:lgs3vdhpazbqpbt57mz3td6cd4

The complex portal - an encyclopaedia of macromolecular complexes

Birgit H.M. Meldal, Oscar Forner-Martinez, Maria C. Costanzo, Jose Dana, Janos Demeter, Marine Dumousseau, Selina S. Dwight, Anna Gaulton, Luana Licata, Anna N. Melidoni, Sylvie Ricard-Blum, Bernd Roechert (+6 others)
2014 Nucleic Acids Research  
The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/ complex), through which protein complexes from major  ...  model organisms are being collated and made available for search, viewing and download.  ...  Model organism groups, such as Saccharomyces Genome Database (11) and WormBase (12) , are contributing expertise and curation effort within their organism of interest, while the MINT database is augmenting  ... 
doi:10.1093/nar/gku975 pmid:25313161 pmcid:PMC4384031 fatcat:afmhddxkfbg7rm2rp5yjgj4fyi

Data publication consensus and controversies

John Kratz, Carly Strasser
2014 F1000Research  
"Ocean Biodiversity Informatics" enabling a new era in marine biology research and management. 316, 203-214.  ...  Nature. 2014. Publisher Full Text 11. Tabuchi H: One author of a startling stem cell study calls for its retraction. The New York Times. 2014. Reference Source 1. 2. 3.  ...  A certain view is implied by the organization of the paper and the references chosen, but they could be more explicit.  ... 
doi:10.12688/f1000research.3979.3 pmid:25075301 pmcid:PMC4097345 fatcat:ltvifnlbxnbslacz6azucs4gea

Data publication consensus and controversies

John Kratz, Carly Strasser
2014 F1000Research  
"Ocean Biodiversity Informatics" enabling a new era in marine biology research and management. 316, 203-214.  ...  The Value of Research Data -Metrics for datasets from a cultural and technical point of view.  ...  The first two types are relatively new and they represent very little of the data actually being published or released today.  ... 
doi:10.12688/f1000research.3979.2 pmid:25075301 pmcid:PMC4097345 fatcat:dmoqila2eneutfsvirru5uawmu

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

Joanna S. Amberger, Carol A. Bocchini, François Schiettecatte, Alan F. Scott, Ada Hamosh
2014 Nucleic Acids Research  
Phenotypic series have been created to facilitate viewing genetic heterogeneity of phenotypes.  ...  Online Mendelian Inheritance in Man, OMIM R , is a comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them.  ...  As of 30 October 2014, OMIM is comprised of over 22,634 entries describing 14,831 genes and 7,894 phenotypes.  ... 
doi:10.1093/nar/gku1205 pmid:25428349 pmcid:PMC4383985 fatcat:ckyogfthmbeg3mpqro5ms2byna

Enhanced Publications: Data Models and Information Systems

Alessia Bardi, Paolo Manghi
2014 Liber Quarterly: The Journal of European Research Libraries  
Enhanced publications" are commonly intended as digital publications that consist of a mandatory narrative part (the description of the research conducted) plus related "parts", such as datasets, other  ...  The state-of-the-art on information systems for enhanced publica tions has today reached the point where some kind of common understanding is required, in order to provide the methodology and language  ...  Acknowledgements This work is partially supported by the European Commission as part of the project OpenAIREplus (FP7-INFRA-2011-2, Grant Agreement no. 283595).  ... 
doi:10.18352/lq.8445 fatcat:6sg3xtzshbfk5kslr5y2zgunwy

DNA Query Language DNAQL: A Novel Approach

Adekunle Y.A, Ogunwobi Z., Alao O.D, Efuwape B.T, Ebiesuwa Seun, Ainam Jean-Paul
2014 International Journal of Computer Applications Technology and Research  
The paper introduces a new layer between the user application which serves as the interface and the database layer.  ...  This paper produces a DNA Query language for querying DNA database in an expressive and concise manner.One of the objectives of this paper was to demonstrate how such a research will be beneficial to biochemistry  ...  update authorization to support data curation via contentbased authorization, in contrast to identity-based authorization, and (4) new access methods and their supporting operators that support pattern  ... 
doi:10.7753/ijcatr0310.1009 fatcat:du5zmjjjrvd3be6hurtph2mb24

Impact of Next-Generation Technologies on Exploring Socioeconomically Important Parasites and Developing New Interventions [chapter]

Cinzia Cantacessi, Andreas Hofmann, Bronwyn E. Campbell, Robin B. Gasser
2014 Msphere  
the development of new interventions to combat parasitic diseases.  ...  step to understanding their biology, as well as interactions with their host(s) and disease.  ...  Acknowledgements Funding from the Australian Research Council, the National Health and Medical Research Council, the Australian Academy of Science, the Alexander von Humboldt Foundation, the Australian-American  ... 
doi:10.1007/978-1-4939-2004-4_31 pmid:25399114 fatcat:viyzkpcf2fcn5exyx2ixq3cfw4
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