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Ontology Driven Data Collection for EuPathDB

Jie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.
2011 International Conference on Biomedical Ontology  
dblp:conf/icbo/ZhengHS11 fatcat:bsl2rbu5rnc7pmffecu3b2aste

EuPathDB: the eukaryotic pathogen genomics database resource

Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb (+18 others)
2016 Nucleic Acids Research  
for private analyses of a user's data.  ...  The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and  ...  ACKNOWLEDGEMENTS The authors wish to thank members of the EuPathDB research communities for their willingness to share genomicscale data sets, often prior to publication and for numerous comments and suggestions  ... 
doi:10.1093/nar/gkw1105 pmid:27903906 pmcid:PMC5210576 fatcat:gp4twmzt7rh2be7oga6xfszwpi

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource [chapter]

Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb, Jessica C. Kissinger, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco
2018 Msphere  
for private analyses of a user's data.  ...  The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and  ...  ACKNOWLEDGEMENTS The authors wish to thank members of the EuPathDB research communities for their willingness to share genomicscale data sets, often prior to publication and for numerous comments and suggestions  ... 
doi:10.1007/978-1-4939-7737-6_5 pmid:29761457 fatcat:c6zfevdra5c7xn7f3qozklsy6i

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

Francislon S Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C Kissinger, Brian P Brunk, Christian J Stoeckert, Gabriel R Fernandes, David S Roos (+1 others)
2017 Nucleic Acids Research  
The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples  ...  MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http:// EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows  ...  User-provided sample details are mapped to an OBO Foundry ontology to expand a EuPathDB local application ontology.  ... 
doi:10.1093/nar/gkx1027 pmid:29106667 pmcid:PMC5753346 fatcat:224de7cw5zd73onvzrjmloydxi

GeneDB--an annotation database for pathogens

F. J. Logan-Klumpler, N. De Silva, U. Boehme, M. B. Rogers, G. Velarde, J. A. McQuillan, T. Carver, M. Aslett, C. Olsen, S. Subramanian, I. Phan, C. Farris (+16 others)
2011 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors wish to acknowledge the contribution of numerous members of the parasitology research community, in the form of advice, suggestions and/or data.  ...  This is in part because GeneDB generates and hosts only genomic data (as opposed to the more complex collections of data sets hosted by EuPathDB), with the focus on keeping these essential data sets accurate  ...  Able to represent ontologies, by the means of CV term relationships, it can make use of any of the ontologies for annotating biological data (Open Biological Ontologies; http://www.obofoundry.org).  ... 
doi:10.1093/nar/gkr1032 pmid:22116062 pmcid:PMC3245030 fatcat:4znikrcq3zbxjizxzokpcjullm

The Ontology for Biomedical Investigations

Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel (+33 others)
2016 PLoS ONE  
OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)).  ...  The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are  ...  OBI is used for categories of terms needed (e.g., sequence data) and for relating the information collected on the form for loading into a database and subsequent data mining.  ... 
doi:10.1371/journal.pone.0154556 pmid:27128319 pmcid:PMC4851331 fatcat:cxeglm5tynfszjthzt7ebbsjhe

Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins

Chi-Ching Lee, Po-Jung Huang, Yuan-Ming Yeh, Sin-You Chen, Cheng-Hsun Chiu, Wei-Hung Cheng, Petrus Tang
2019 BMC Bioinformatics  
Conclusions: The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface.  ...  Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist.  ...  Availability of data and materials The web site of PPTdb is freely accessible at http://pptdb.cgu.edu.tw.  ... 
doi:10.1186/s12859-019-2857-7 fatcat:dwao5azjifdvdkiwtogbrn2tqe

The strategies WDK: a graphical search interface and web development kit for functional genomics databases

S. Fischer, C. Aurrecoechea, B. P. Brunk, X. Gao, O. S. Harb, E. T. Kraemer, C. Pennington, C. Treatman, J. C. Kissinger, D. S. Roos, C. J. Stoeckert
2011 Database: The Journal of Biological Databases and Curation  
The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects.  ...  With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets.  ...  Acknowledgments We wish to thank EuPathDB users and beta-testers, and collaborators interested in adopting the Strategies/WDK system in other bioinformatics applications, for their many helpful comments  ... 
doi:10.1093/database/bar027 pmid:21705364 pmcid:PMC3122067 fatcat:q5kvwywmqbbsrfbnbz6g2br7iq

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

Emmanuel Ruhamyankaka, Brian P. Brunk, Grant Dorsey, Omar S. Harb, Danica A. Helb, John Judkins, Jessica C. Kissinger, Brianna Lindsay, David S. Roos, Emmanuel James San, Christian J. Stoeckert, Jie Zheng (+1 others)
2019 Gates Open Research  
(EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related species, and select hosts) combined with a unified semantic web framework.  ...  Supporting study documentation aids contextualization, and data can be downloaded for advanced analyses.  ...  We thank the data providers for their time and dedication, which aided public release of data on ClinEpiDB, and we thank the EuPathDB team for their work on extending the architecture and developing the  ... 
doi:10.12688/gatesopenres.13087.1 pmid:32047873 pmcid:PMC6993508 fatcat:u3rviq57fncdnlbe65vplnva6i

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

Emmanuel Ruhamyankaka, Brian P. Brunk, Grant Dorsey, Omar S. Harb, Danica A. Helb, John Judkins, Jessica C. Kissinger, Brianna Lindsay, David S. Roos, Emmanuel James San, Christian J. Stoeckert, Jie Zheng (+1 others)
2020 Gates Open Research  
studies by leveraging the extensive web toolkit and infrastructure of the Eukaryotic Pathogen Database Resources (EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related  ...  Supporting study documentation aids contextualization, and data can be downloaded for advanced analyses.  ...  We thank the data providers for their time and dedication, which aided public release of data on ClinEpiDB, and we thank the EuPathDB team for their work on extending the architecture and developing the  ... 
doi:10.12688/gatesopenres.13087.2 fatcat:gmul6zzsejgaljkysuvfh5t2zm

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Priti P. Parikh, Todd A. Minning, Vinh Nguyen, Sarasi Lalithsena, Amir H. Asiaee, Satya S. Sahoo, Prashant Doshi, Rick Tarleton, Amit P. Sheth, Aaron R. Jex
2012 PLoS Neglected Tropical Diseases  
The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee  ...  Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring indepth computer  ...  Acknowledgments We would like to thank Harshal Patni at the Kno.e.sis Center for his help with the Web forms, Matthan Sink for some figures and Trykipedia updates, and Brent Weatherly for initial work  ... 
doi:10.1371/journal.pntd.0001458 pmid:22272365 pmcid:PMC3260319 fatcat:lg47t2f42jcv7pfaqldn7wibo4

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

Vivien G. Dugan, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Ruchi M. Newman, Brett E. Pickett, Lynn M. Schriml, Timothy B. Stockwell, Christian J. Stoeckert, Dan E. Sullivan, Indresh Singh, Doyle V. Ward (+47 others)
2014 PLoS ONE  
To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and  ...  It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology  ...  Acknowledgments We are grateful to the various data providers for their participation in the definition of important metadata to capture for sequencing projects.  ... 
doi:10.1371/journal.pone.0099979 pmid:24936976 pmcid:PMC4061050 fatcat:xr3rkfcxtndi7owhcl6k6mmiyi

SilkPathDB: a comprehensive resource for the study of silkworm pathogens

Tian Li, Guo-Qing Pan, Charles R. Vossbrinck, Jin-Shan Xu, Chun-Feng Li, Jie Chen, Meng-Xian Long, Ming Yang, Xiao-Fei Xu, Chen Xu, Bettina A. Debrunner-Vossbrinck, Ze-Yang Zhou
2017 Database: The Journal of Biological Databases and Curation  
We have collected genomic data for 86 silkworm pathogens from 4 taxa (fungi, microsporidia, bacteria and viruses) and from 4 lepidopteran hosts, and developed the open-access Silkworm Pathogen Database  ...  This will facilitate the reuse of these data for further analysis.  ...  They would like to thank the anonymous reviewers for their valuable comments and suggestions. Conflict of interest. None declared.  ... 
doi:10.1093/database/bax001 pmid:28365723 pmcid:PMC5467577 fatcat:zukstmg5rjdrpnyc4arizpbrja

Infectious Disease Ontology [chapter]

Lindsay Grey Cowell, Barry Smith
2009 Infectious Disease Informatics  
The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information.  ...  More recently, ontologies have been shown to have significant benefits both for the analysis of data resulting from high-throughput technologies and for automated reasoning applications, and this has led  ...  applications used for clinical data collection.  ... 
doi:10.1007/978-1-4419-1327-2_19 fatcat:ouv6gfucszfcpdh5mlifysopne

ChlamBase: a curated model organism database for the Chlamydia research community

2019 Database: The Journal of Biological Databases and Curation  
ChlamBase was designed to serve as a central access point for genomic and proteomic information for the Chlamydia research community.  ...  In addition, a key feature of ChlamBase is that it empowers users in the field to contribute new annotations and data as the field advances with continued discoveries.  ...  for Gene Expression Data, InterPro Domains, Host-Pathogen Interaction Data, Gene Ontology Annotations, Operons and Mutants ( Figure 3A ).  ... 
doi:10.1093/database/baz041 pmid:30985891 pmcid:PMC6463448 fatcat:qtflnse2zreyfpqmwp6ibm6o5m
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