Browse a selection of projects that use BioPortal resources
| Project | Description | Contacts | Institutions | Ontologies |
|---|---|---|---|---|
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Access of OntoKBCF via a CCR-based EHR prototype
Home Page |
This is an exploration of introducing molecular genetic information into a simulated clinical setting- a Continuity of Care Record (CCR)... | Xia Jing, Stephen Kay, Nicholas Hardiker, Tom Marley, James Cimino | The University of Salford, NIH | 1 |
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AdaptEHR
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Adaptive EHR (AdaptEHR) is built upon a context-based framework, integrating data from different sources in the patient record and subsequently... | University of California, Los Angeles | 3 | |
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Adverse Event Reporting Ontology (AERO)
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The Adverse Event Reporting Ontology (AERO) is an ontology aimed at providing logical representation of adverse events guidelines, increasing quality and accuracy of reported events. | Melanie Courtot | 6 | |
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agriGO
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The agriGO is an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. | China Agricultural University | 1 | |
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AmiGO
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AmiGO is the official web-based set tools for searching and browsing the Gene Ontology database, which consists of a controlled... | Gene Ontology Consortium | 1 | |
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An Ontology for Drug Discovery Investigations
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The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to... | Da Qi, Larisa Soldatova, Ross King, Andrew Hopkins, Richard Bickerton | Aberystwyth University | 5 |
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AnoBase
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AnoBase is a database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world's most important... | 2 | ||
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AQUAEXCEL
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AQUAEXCEL aims to integrate key aquaculture research infrastructures across Europe, in order to promote their coordinated use and development. | FP7, Capacities; Research Infrastructures | 1 | |
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Assay Annotation
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Excel template uses BAO to annotated data into PubChem's Deposition System. The template provides dropdown lists for fields where the value is allowed (controlled vocabulary). | S. Schurer, U. Vempati, S. Canny, M. Southern | TSRI and UM | 1 |
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AstraZeneca HTS annotation
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As a part of the AstraZeneca in kind contribution to the IMI OpenPhacts project, AstraZeneca HTS data is annotated according to the BAO ontology. | L. Zander Balderud, O. Engkvist, M. Bjäreland, N. Blomberg | AstraZeneca R&D | 1 |
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BAOSearch
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BAOSearch is a web-based application for querying, browsing and downloading small molecule biological screening results, including high-throughput screening (HTS) data.... | Mader C, Datar N, Abeyruwan S, Koleti A, Venkatapuram S, Chung C, Puram D, Vempati U, Sakurai K, Przydzial M, Lemmon V, Visser U, Schurer S. | University of Miami | 1 |
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Bgee
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Bgee is a database to compare expression patterns between animals. We create homology relationships between anatomical ontologies, and store this... | Robinson-Rechavi lab | Universite de Lausanne | 12 |
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Bio2RDF
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The Bio2RDF project transforms silos of life science data into a globally distributed network of linked data for biological knowledge discovery. | Michel Dumontier, Peter Ansell, Francois Belleau, Allison Callahan, Jacques Corbeil, Jose Cruz-Toledo, Alex De Leon, Steve Etlinger, James Hogan, Nichealla Keath, Jean Morissette, Marc-Alexandre Nolin, Nicole Tourigny, Philippe Rigault and, Â Paul Roe | Multi | 1 |
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BioAssay Ontology
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The BioAssay Ontology (BAO) is an NIH-funded project to develop standard terminologies and a formal, extensible, knowledge-based description of biological... | University of Miami | 6 | |
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Bioconductor
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Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language. | 1 | ||
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Biodiversity Information Standards
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This project will provide a public space for reviewing and commenting on the ontologies related to biodiversity information standards such as TDWG Ontology, Darwin-SW, TaxonConcept, and the Biological Collections Ontology (BCO). | Ramona Walls, John Deck | 4 | |
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Bioinformatics Web Service Ontology
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The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services. | Jie Zheng, Alok Dhamanaskar | University of Pennsylvania, University of Georgia | 4 |
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BioLit
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A web database of open access articles with metadata | Lynn Fink | UCSD | 0 |
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BioPAX
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The goal of the BioPAX group is to develop a common exchange format for biological pathways data. ... | 1 | ||
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Biositemaps
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The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org) has developed technologies to address... | 1 | ||
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BioXSD
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BioXSD defines exchange formats of basic bioinformatics types of data. It is a rich, but not too complicated XML-Schema-based format... | Matus Kalas, Edita Karosiene, Pal Puntervoll, Sveinung Gundersen, Jon Ison, Christophe Blanchet, Kristoffer Rapacki, Inge Jonassen ... | University of Bergen, Danish Technical University, CNRS, EBI ... | 1 |
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Blood Ontology
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The Blood Ontology is a set of co-related ontologies being created to gather and represent data about blood according to well-founded ontological principles. | HTLV Interdisciplinar Research Group | Federal University of Minas Gerais, Hemominas Foundation | 7 |
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breast tissue cell lines
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Contains a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built... | Usha Mahadevan & Arathi Raghunath | Molecular Connection Pvt. Ltd. | 0 |
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caB2B
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caB2B, or cancer Bench-to-Bedside, is a tool that enables querying for cancer related information hosted anywhere on caGrid. It... | National Cancer Institute | 1 | |
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CBO
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Create Cell Behavior Ontology | 1 | ||
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Cell cycle events
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Notable Cell Cycle events that can be tested with HTS-HCS modes | unc chapel hill | 4 | |
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Cell line ontology
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Cell lines are key experimental models to understand protein interactions and signaling pathways. With a large pool of such... | Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan | Molecular Connections Pvt. Ltd | 3 |
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Cell line ontology
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Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive... | Usha Mahadevan | Molecular Connections Pvt. Ltd. | 3 |
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CGAP GO Browser
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With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. | Cancer Genome Anatomy Project | 1 | |
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ChEMBL-RDF
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RDF version of the CC-BY-SA ChEMBL database developed at the EBI in the group of John Overington. | Maastricht University | 2 | |
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Chemical Information Ontology
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The Chemical Information Ontology (CHEMINF) is an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic, observed or computed. | Leonid Chepelev, Michel Dumontier, Janna Hastings, Egon Willighagen | multi | 1 |
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Clinical Genomicist Workstation
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The advent of genome-wide profiling technologies and their routine use in basic science and translational research is now promoting their... | 1 | ||
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COBrA
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COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts... | 1 | ||
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Comparative Toxicogenomics Database
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A public database that enhances understanding about the effects of environmental chemicals on human health. Integrated GO data and a... | 1 | ||
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CTSA Inventory Resource Web Presence (CIRWP)
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The CTSA Inventory Resource Web Presence (CIRWP) is a federated, inter-institutional project to facilitate resource discovery. The CIRWP project contains... | 1 | ||
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Darwin Core (DwC)
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The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called... | TDWG Darwin Core Task Group | Biodiversity Information Standards (TDWG) | 3 |
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dictyBase
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An Online Informatics Resource for Dictyostelium. | 1 | ||
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DSS
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Decision Support for Arthropod-borne Infectious Diseases. The Ontology portion of our project is still under construction. | David Penhall, Saul Lozano-Fuentes | Colorado State University | 2 |
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Dynamic enhancement of drug product labels
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Demonstrate a novel approach to updating and expanding upon information present in drug product labels that is useful for determining... | Scientific Discourse Task Force | W3C Health Care and Life Sciences Interest Group | 1 |
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DynGO
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DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users... | 1 | ||
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eagle-i
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The eagle-i project is building a searchable network of research resources at research institutions nationwide. We are developing an application... | Melissa Haendel, Carlo Torniai | Consortium | 15 |
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EFO
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The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has... | James Malone, Helen Parkinson | EBI | 1 |
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Electronic Trial Master File - eTMF
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This preliminary version of the eTMF content model ontology is designed to support clinical trial regulatory content management and eArchive... | Zachariah Schmidt | CareLex - a Non-profit for Content Archive Resource Exchange | 2 |
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Electrophysiology Ontology
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The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to... | Dr. Raimond L. Winslow, Stephen J. Granite | The Johns Hopkins University | 7 |
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EMBOSS
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The European Molecular Biology Open Software Suite (EMBOSS) is a well established, high quality package of open source software tools for molecular biology. | Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag | EMBL-EBI | 1 |
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eMERGE - eleMAP
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Organized by the National Human Genome Research Institute (NHGRI) with additional funding from the National Institute of General Medical Sciences,... | 0 | ||
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Epidemiology Term Annotation
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This script will map commonly used epidemiology variables to SNOMED or LOINC concepts | 2 | ||
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Epilepsiae
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EPILEPSIAE- Evolving Platform for Improving the Living Expectations for Patients Suffering from IctAl Events is developing the European Database on... | partners from 4 countries | EU FP7 | 1 |
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Epiwork - Epidemic Marketplace
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The Epidemic Marketplace is a data integration platform where epidemiological data and related resources are stored, managed and made available, fostering collaboration. | Fundacao da Faculdade de Ciencias da Universidade de Lisboa | 12 | |
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eSysbio
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eSysbio is a project for developing an online workbench for collaborative computational biology research. It provides a secure Web-based workspace... | Kidane Tekle, Hakon Sagehaug, Matus Kalas, Siv Midtun Hollup, Michael Dondrup, Anne-Kristin Stavrum, Pawel Sztromwasser, Armin Topfer, Kjell Petersen, Inge Jonassen, Pal Puntervoll | University of Bergen | 2 |
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Evaluation of LOINC Document Ontology
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Use of LOINC Document Ontology to facilitate NLP projects, Health Information Exchange and secondary use of data | National Institute of Health Clinical Center | 1 | |
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Evidence Ontology
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The Evidence Ontology (ECO) is a controlled vocabulary that describes types of scientific evidence within the realm of biological research... | Marcus Chibucos & Michelle Giglio | Institute for Genome Sciences | 1 |
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Exterminator nassau county ny
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Exterminator nassau county ny | 0 | ||
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FGED-MGED Ontology
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The Functional Genomics Data (FGED) Society has incorporated the MGED Ontology (MO) into OBI for use in annotating functional genomics studies especially with the MAGE-TAB format. | 2 | ||
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Fishmap
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FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. | 1 | ||
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FlyBase
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The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico. | The FlyBase Consortium | 1 | |
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Fundamental Biology of Sudden Cardiac Death and Its Application to Identify Patients at Risk (PROSE-ICD)
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This study examines the role of genetic, protein and electrocardiographic markers measured longitudinally in predicting the risk of SCD and overall mortality in patients with implantable defibrillators placed for primary prevention. | Gordon Tomaselli (PI) | Johns Hopkins Hospital, Washington Hospital Center, Virginia College of Medicine | 1 |
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G PROTEIN-COUPLED RECEPTOR (GPCR) BIOASSAYS
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The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of... | Przydzial M, Bhhatarai B, Koleti A, Schurer S. | University of Miami | 4 |
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Gemma
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Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data,... | Dr. Paul Pavlidis | University of British Columbia | 9 |
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Gene Ontology Browsing Utility (GOBU)
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Gene Ontology Browsing Utility (GOBU). GOBU is a Java-based software program for integrating biological annotation catalogs under an extendable software... | 1 | ||
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Gene Ontology Consortium
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The GO Consortium is the set of model organism and protein databases and biological research communities actively involved in the development and application of the Gene Ontology. | Gene Ontology Consortium | 1 | |
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Gene Ontology For Functional Analysis (GOFFA)
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Gene Ontology For Functional Analysis (GOFFA) is a tool developed for ArrayTrack that takes a list of genes and identifies... | 1 | ||
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Gene Ontology Normal Usage Tracking System (GONUTS)
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This Gene Ontology Normal Usage Tracking System (GONUTS) is a wiki where users of the Gene Ontology can contribute and... | 1 | ||
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GeneInfoViz
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GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of... | 1 | ||
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GeneTools
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GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this... | Norwegian University of Science and Technology | 1 | |
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GenNav
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GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. | 1 | ||
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GOblet
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GOblet is a software package that performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses... | 1 | ||
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GoFish
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The GoFish program, available as a Java applet online or to download, allows the user to construct arbitrary Boolean queries... | University of Toronto; Ontario; Canada, Harvard Medical School; Massachusetts; USA | 1 | |
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GOProfiler
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GOProfiler provides a summary of the GO annotations available in AgBase. The user provides a species (taxon id) and GOProfiler... | 1 | ||
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GOSlimViewer
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GOSlimViewer is used to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs. | 1 | ||
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Gramene
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As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which... | 6 | ||
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GRANATUM
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The vision of the GRANATUM project is to bridge the information, knowledge and collaboration gap among biomedical researchers in Europe... | 1 | ||
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Hewan Invertebrata
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Ontology hewan Invertebrata | Vasko Edo Gultom | 2 | |
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HOM - Health Ontology Mapper
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HOM’s open source components provide a key framework for mapping data, requesting data and delivering data to and from data... | Rob Wynden, Prakash Lakshminarayanan, Ketty Mobed | UCSF | 21 |
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Human Protein Ontology
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This project aims at developing a protein ontology of human proteins for different semantic queries. Proteins are categorized based on... | Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan | Molecular Connections Pvt. Ltd | 0 |
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Hypertrophic Cardiomyopathy
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The Hypertrophic Cardiomyopathy (HCM) project is focused on the prognosis of HCM, i.e on the prediction of the possible outcome... | 4 | ||
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Hypertrophic Cardiomyopathy consortium
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The Hypertrophic Cardiomyopathy Consortium is a network of investigators focused on the research, diagnosis, and treatment of HCM. The Consortium... | Theodore Abraham, MD | Johns Hopkins University | 1 |
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iBeetle
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The iBeetle projects is a large scale RNAi screening project in the red flour beetle Tribolium castaneum. Using the RNA... | Gregor Bucher, Martin Klinger | Georg-August University Goettingen, Friedrich-Alexander University Erlangen-Nürnberg | 2 |
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Image & Data Quality Assessment
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An ontology for assessment of image and data quality | University of Applied Sciences Brandenburg | 0 | |
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Immune Epitope Database
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The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. | IEDB Contacts | La Jolla Institute for Allergy & Immunology | 1 |
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Immunology Database and Analysis Portal (ImmPort)
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ImmPort, the Immunology Database and Analysis Portal, is a one stop shop to access reference and experiment data for immunologists.... | Richard H. Scheuermann, et al. | U.T. Southwestern Medical Center | 5 |
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Influenza Ontology
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The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO). | Burke Squires, Lynn Schriml, Joanne Luciano | UT Southwestern, Univ of Maryland, MITRE | 8 |
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Influenza Research Database (IRD)
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The mission of the Influenza Research Database (IRD) is to provide a resource for the influenza virus research community that... | Richard H. Scheuermann, et al. | J. Craig Venter Institute | 8 |
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Integrative Genomics
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Integration of high-dimensional genomic and phenomic data is challenged with scalability and semantic robustness for intuitive querying. To address these... | James Chen, Arka Pattanayak, Chaitanya Shivade | The Ohio State University | 18 |
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Integrative Tools for Protozoan Parasite Research (ITPPR)
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The Integrative Tools for Protozoan Parasite Research project is using OBI to develop forms to capture structured meta-data about studies... | Christian Stoeckert | University of Pennsylvania | 1 |
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International Fanconi Anemia Registry (IFAR)
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The International Fanconi Anemia Registry (IFAR) was started in 1982 at The Rockefeller University by Dr. Arleen Auerbach. The... | Erica Sanborn, Agata Smogorzewska, Arleen Auerbach, Francis Lach, Edward Barbour, Shamim Mollah, Sajin Balakrishnan, Ummey Johra | Rockefeller University | 5 |
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ISA software suite
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An open source ISA software suite and an extensible hierarchical data structure implemented by a growing number of international public... | International collaborative effort | Multiple institutions; leads at University of Oxford, UK | 37 |
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Kino
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Kino is an integrated suite of tools that enables scientists to annotate biological related web-based documents. It can annotate documents... | Amit Sheth, Ajith Ranabahu, Maryam Panahiazar | Ohio Center of Excellence in Knowledge-enabled Computing (Kno.e.sis) | 7 |
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LogMap
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Logic-based and Scalable Ontology Matching. LogMap is a highly scalable ontology matching system with `built-in' reasoning and diagnosis capabilities. Currently,... | Ernesto Jimenez Ruiz and Bernardo Cuenca Grau | University of Oxford | 4 |
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Lowongan Kerja Terbaru 2013
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Lowongan Kerja, Lowongan Kerja Terbaru 2013, Lowongan Bank, Lowongan BUMN, Lowongan CPNS 2013, Lowongan Pertamina, Lowongan Telkom, Lowongan Kereta Api, Lowongan Astra, Lowongan Guru, Lowongan SMA sederajat | duakerja | blogger | 2 |
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Manatee
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Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic... | J. Craig Venter Institute, University of Maryland School of Medicine | 1 | |
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maryan zirkle
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working PTSD ontology | ohsu | 1 | |
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Medical Dictionary
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Medical annotator & dictionary | Dalhousie University | 2 | |
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Mental Functioning Ontology
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The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as... | Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan | University of Geneva, University at Buffalo | 2 |
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MeRy-B
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MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants. This database is involved in the ISA commons project (isacommons.org). | Daniel Jacob, Catherine Deborde, Annick Moing | INRA & Univ. Bordeaux | 21 |
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MGI GO Browser
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With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the... | Mouse Genome Informatics, The Jackson Laboratory | 1 | |
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miRNAO
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An application ontology for microRNAs. | 0 | ||
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Mobile RadLex
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A mobile browser of RadLex for the Android Phone. Free to download on the Android Market. :D | Mantas | 1 | |
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Mouse Genome Informatics
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MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the... | 1 | ||
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Multiscale Ontology for Skin Physiology
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The purpose of this project is to investigate the representation of physiological processes in the skin across levels of spatial scale. | Tariq Abdulla | Loughborough University | 0 |
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nano-TAB
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The nano-TAB standard specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with... | 1 | ||
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NBTontology
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The NBTontology is used to describe Neurophysiological Biomarkers in the Neurophysiological Biomarker Toolbox (NBT) | 0 | ||
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NCBO Annotator
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A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the... | NCBO | Stanford University | 121 |
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NCBO Resource Index
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The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key... | NCBO | Stanford University | 152 |
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Network Ontology Analysis (NOA)
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Network Ontology Analysis (NOA) is a freely available collection of Gene Ontology tools aiming to analyze functions of gene network... | Chinese Academy of Sciences | 1 | |
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NeuMORE
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Develop an ontology in recovery domain. | University of South Alabama | 1 | |
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Neural ElectroMagnetic Ontologies (NEMO)
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NEMO is developing ontologies for representation and integration of event-related brain potentials (ERPs). To support this work, we are developing... | NEMO core (Gwen Frishkoff, Robert Frank, Paea LePendu, Haishan Liu, Dejing Dou, Allen Malony, Jason Sydes, Nathan Dunn); NEMO ERP Consortium (Gwen Frishkoff, Tim Curran, Dennis Molfese, John Connolly, Kerry Kilborn, Chuck Perfetti) | University of Oregon & Georgia State University | 22 |
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Neurocarta
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Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of... | Dr. Paul Pavlidis | University of British Columbia | 3 |
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Neuroscience Information Framework
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The Neuroscience Information Framework (NIF; http://nif.nih.gov) is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any... | Maryann Martone, Jeffrey Grethe, Amarnath Gupta, Gordon Shepherd, Giorgio Ascoli, Paul Sternberg, David Van Essen | 9 | |
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Nobish1
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Nothing | 2 | ||
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Nomenclature for Anatomic Pathology (NAP)
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Unifying Nomenclature for Anatomic Pathology in Italy | Arrigo Bondi | SIAPEC-IAP | 5 |
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NViz: A Visualization Tool for Refining Mappings between Biomedical Ontologies
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Ontology alignment, the task of identifying mappings between ontologies, is a key task for knowledge sharing between applications that use... | Watson W.K. Chua, Jung-jae Kim, Bui Duc Hieu | Nanyang Technological University | 2 |
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OBO-Edit
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OBO-Edit is an open source, platform-independent application written in Java for viewing and editing any OBO format ontologies. OBO-Edit is... | Gene Ontology Consortium | 1 | |
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Onto-Compare
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Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously.... | Wayne State University | 1 | |
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Onto-Design
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Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on... | Wayne State University | 1 | |
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Onto-Express
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The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially... | Wayne State University | 1 | |
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OntoCAT
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High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. | Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz | EMBL-EBI, University of Groningen | 270 |
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OntoCOG
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Ontology based web service for COG enrichment study by using Fisher's exact test. | Yu Lin, Yongqun He, Zuoshuang Xiang | University of Michigan | 2 |
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Ontologi Hewan Invertebrata
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ok. i had create it for benefit in future also science too. so greatful to rdf/owl in semantic web. | VASKO EDO GULTOM | universitas sumatera utara | 1 |
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Ontologi Hewan Invertebrata
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I am A Student Bachelor Of IT. | VASKO EDO GULTOM | USU | 1 |
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Ontology Evolution Explorer (OnEx)
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The Ontology Evolution Explorer (OnEx) is a web-based system for exploring ontology changes. It provides access to several versions of... | University of Leipzig | 2 | |
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Ontology of Data Mining (OntoDM)
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OntoDM is a general-purpose ontology for the domain of data mining. The ontology includes the information processing processes that occur... | Pance Panov, Saso Dzeroski, Larisa Soldatova | Jozef Stefan Institute | 7 |
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Ontology-based knowledge base model-OntoKBCF
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This is a knowledge base model including both molecular genetic information and health information of cystic fibrosis. Another main component... | Xia Jing, Stephen Kay, Nicholas Hardiker, Tom Marley | The University of Salford | 1 |
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OntoMaton
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OntoMaton is a google spreadsheet application allowing for ontology search and tagging directly within google spreadsheets. More information can be found here: https://github.com/ISA-tools/OntoMaton | ISA team | Oxford University | 312 |
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OntoVisT
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OntoVisT is a general purpose ontological visualization tool. Ontologies have emerged as a fast growing research topic in the area... | Jawaharlal Nehru University | 1 | |
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Open PHACTS
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Open PHACTS (Open Pharmacological Concepts Triple Store) is a knowledge management project of the Innovative Medicines Initiative (IMI), a unique... | 6 | ||
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Panacea
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“Panacea†aims to build an intelligent recommendation system to effectively propose drug therapies that will support and facilitate health... | 5 | Ergobyte Informatics S.A. | 2 |
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Pandora - Protein ANnotation Diagram ORiented Analysis
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With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological... | Hebrew University of Jerusalem | 1 | |
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ParameciumDB
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ParameciumDB is a new model organism database associated with the genome sequencing project. Built with core components of the Generic... | 1 | ||
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Pathway Portal
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The Pathway Portal is a multi-tier approach offering dynamic graphic representation of pathways along with associated annotations, integration with other... | Victoria Petri | Medical College of Wisconsin | 1 |
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Patient/Research Participant Permissions Ontology
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An ontology to capture patients' and research participants' research permissions, consents and routine care permissions. | MUSC | 1 | |
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Pediatric Terminology
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Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age. | Ranjana Srivastava, Daniel Lyman, Ipsita Das | National Institute of Child Health and Human Development | 1 |
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PhenoMiner
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PhenoMiner is a database and software system integrating rat phenotype measurement data from multiple projects and experiments. It uses 3 ontologies to standardize data. | Mary Shimoyama, Melinda Dwinell | Medical College of Wisconsin | 3 |
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PhenoMiner
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PhenoMiner integrates rat phenotype measurement data | Rajni Nigam, Mary Shimoyama, Melinda Dwinell | RGD | 4 |
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Phenoscape
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What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach... | Paula Mabee, Monte Westerfield, Todd Vision, Hilmar Lapp, Wasila Dahdul, James Balhoff, Peter Midford | National Evolutionary Synthesis Center, University of South Dakota, University of Oregon, University of North Carolina at Chapel Hill | 9 |
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PID PhenomeR
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PID phenomer is a web-based integrated platform for collection, mapping, storage and visualization of observed phenotypic terms for primary immunodeficiency... | RCAI Immunoinformatics Research Unit | The Institute of Physical and Chemical Research (RIKEN), Yokohama | 6 |
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PID PhenomeR
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PID phenomer is a web-based integrated platform for collection, mapping, storage and visualization of observed phenotypic terms for primary immunodeficiency diseases (PIDs). | 0 | ||
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Plant Ontology
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The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomical and morphological structures and growth and developmental stages... | Oregon State University | 18 | |
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Portfolio Management Application (PMA)
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PMA is a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports | 0 | ||
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Protege
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Protege is a free, open source ontology editor and knowledge-base framework. | 0 | ||
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Protein Ontology Project
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PO integrates protein data formats and provide a structured and unified vocabulary to represent proteins. PO provides integration of heterogeneous protein and biological data sources. | Amandeep S. Sidhu | BIOMAP Project Lab | 0 |
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Prov
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The outcome of the W3C Prov group | Helena F. Deus | DERI | 0 |
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PubChem
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Chemical biology resource providing biological activities of small molecules and substances. | NCBI | 7 | |
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QuickGO
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QuickGO is a fast web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at... | European Bioinformatics Institute | 1 | |
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RAD
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My RAD for PhD | farhanjk | Dalhousie University | 1 |
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RadLex
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RadLex is a controlled terminology for radiology. | RSNA | 0 | |
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Reference Sequence Annotation
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Provide ontologies to describe sequence annotations, reference sequences, and how to link annotations across references. | Zuotian Tatum, Andrew Gibson, Jeroen F.J. Laros, Marco Roos, Mark Thompson | Leiden University Medical Center | 0 |
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Resource of Asian Primary Immunodeficiency Diseases (RAPID)
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Resource of Asian primary immunodeficiency diseases (RAPID) is a web-based integrated compendium of molecular alterations in primary immunodeficiency disease genes and other pertinent information. | RCAI Immunogenomics group, Immunoinformatics group and IOB group | The Institute of Physical and Chemical Research (RIKEN) Yokohama, Japan & Institute of Bioinformatics (IOB), Bangalore, India | 1 |
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RightField
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RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. For each annotation field, RightField can specify... | Stuart Owen, Katy Wolstencroft, Matthew Horridge, Carole Goble | University of Manchester | 1 |
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SADI
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SADI is a framework to create Semantic Web services using OWL classes as service inputs and outputs | Christopher Baker, Melanie Courtot, Jose Cruz-Toledo, Michel Dumontier, Steve Etlinger, Nichealla Keath, Artjom Klein, Luke McCarthy, Silvane Paixao, Ben Vandervalk, Natalia Villanueva-Rosales, Mark Wilkinson | Multi | 1 |
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SBGN
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Systems Biology Graphical Notation (SBGN), is a visual language developed by a community of biochemists, modelers and computer scientists to allow the represention of networks of biochemical interactions in a standard, unambiguous manner. | SBGN Editors | COMBINE | 1 |
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SBML
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The SBML (systems biology markup language) is a machine-readable, standard exchange format for computational models. It is developed collaboratively with the modelling community to meet their evolving needs. | SBML Editors | COMBINE | 1 |
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SBO
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Systems Biology Ontology | 0 | ||
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Schizosaccharomyces pombe
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This database contains all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs... | 1 | ||
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SED-ML
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The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in... | SED-ML editors | COMBINE | 1 |
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SEEK
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A suite of tools for the management and sharing of Systems Biology resources, such as data, models, SOPs and publications | Stuart Owen, Katy Wolstencroft, Olga Krebbs, Quyen Nguyen, Franco du Preeze, Jacky Snoep, Wolfgang Mueller, Carole Goble | University of Machester / HITS, Heidelberg | 1 |
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SEEK
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SEEK is the SysMO Assets Catalogue. It contains information about who holds what data, models, protocols and expertise, and... | Stuart Owen, Katy Wolstencroft, Olga Krebbs, Quyen Nguyen, Franco du Preeze, Jacky Snoep, Carole Goble | University of Manchester, Heidelberg Institute of Technology | 2 |
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semanticscience integrated ontology
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The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for diverse knowledge representation across physical, processual and informational entities. | Michel Dumontier | Carleton University | 0 |
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SemGen
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SemGen is a software tool for automating the modular composition and decomposition of biosimulation models. It uses BioPortal web services to provide model annotators access to reference ontology terms. | Maxwell Neal, Daniel Cook, John Gennari | University of Washington | 9 |
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Semtools
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The Semantic Tools for Data Management (Semtools) project is tackling critical issues in the management and use of heterogeneous scientific... | Leinfelder, Jones, Schildhauer, O'Brien, Bowers | NCEAS - UCSB | 2 |
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SEQwiki
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The SEQanswers wiki (SEQwiki) is a wiki database that provides an extensive catalogue of tools, technologies and tutorials for high-throughput sequencing (HTS), including information about HTS service providers. | Jing-Woei Li1, Keith Robison, Marcel Martin, Andreas Sjödin, Björn Usadel, Matthew Young, Eric C. Olivares, and Dan M. Bolser | NA | 1 |
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SGD
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SGD(TM) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. | 1 | ||
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SKELETOME
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The aim of the SKELETOME project is to develop a community-driven, ontology-based knowledge curation platform for the skeletal dysplasia domain. | Tudor Groza | School of ITEE, The University of Queensland | 6 |
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Software Tool for Rapid Annotation of Proteins (STRAP)
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The Software Tool for Rapid Annotation of Proteins saves you time by automatically annotating a protein list with information that... | Boston University School of Medicine | 1 | |
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SYSNPs
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SYSNPs allows the user to compile information about all the SNPs in any human gene or genome region of interest... | Institut de Biologia Evolutiva | 1 | |
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TAIR
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The Arabidopsis Information Resource (TAIR) collects information and maintains a database of genetic and molecular biology data for Arabidopsis thaliana, a widely used model plant. | 1 | ||
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TAIR Keyword Browser
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TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to... | The Arabidopsis Information Resource | 1 | |
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The CardioVascular Research Grid (CVRG)
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The aim of the CardioVascular Research Grid (CVRG) project is to create an infrastructure for sharing cardiovascular data and data... | Raimond Winslow, PhD | Johns Hopkins University, Emory University, | 1 |
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The Cognitive Atlas
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The Cognitive Atlas is a collaborative knowledge building project that aims to develop an ontology of mental processes and relate them to the mental tasks that are used to measure them. | Russell Poldrack | University of Texas at Austin/UCLA | 4 |
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The Comparative Data Analysis Ontology
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The objective of this project is to develop an ontology for the description of information relevant to experiments in evolutionary... | Arlin Stoltzfus, Julie Thompson, Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli | NMSU, NIST, University of Strasbourg | 0 |
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The Drug Interaction Knowledge Base
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The Drug Interaction Knowledge Base (DIKB) is a clinically-oriented, evidence-based, knowledge base designed to support pharmacoepidemiology and clinical decision support.... | Richard D Boyce | University of Pittsburgh | 3 |
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The Human Phenotype Ontology
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The human phenotype ontology (HPO) intends to offer a tool that will allow large-scale computational analysis of the human phenome.... | 1 | ||
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The Ontological Discovery Environment
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A web-based environment that discovers ontological structure from empirical data. | Elissa Chesler, Erich Baker, Michael Langston, Jeremy Jay | The Jackson Laboratory | 5 |
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ThomCan: Upper-level Cancer Ontology
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Providing an upper-level ontology for cancer. | Andre Stander | University of Pretoria | 0 |
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Time Event Ontology
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The Time Event Ontology (TEO) is an OWL ontology designed for representing the temporal relations among events and time stamps. | Cui Tao | Mayo Clinic | 0 |
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Tk-GO
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Tk-GO is a GUI wrapping the basic functions of the GO AppHandle library from BDGP. GO terms are presented in... | Illuminae | 1 | |
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Tools for Comparative Phenomics
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Here, we provide a number of tools for the integration, analysis and exploration of phenotypes across species. We currently provide... | 2 | ||
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Toxicological ontology
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toxicological ontology | OpenTox FP7 EU project | 0 | |
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UW Health HIMC
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Health Information Management Center within UW Health. | Nathan S. Wilson, Keith M Wanta | University of Wisconsin | 4 |
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Vaccine Investigation and Online Information Network (VIOLIN)
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Vaccine Investigation and Online Information Network (VIOLIN) is a web-based central resource that integrates vaccine literature data mining, vaccine research... | Yongqun "Oliver" He | University of Michigan | 1 |
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Vector Surveillance and Management Ontology
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Produce candidate ontologies for vector surveillance and vector management with incorporation into a computer system | Saul Lozano-Fuentes, Lars Eisen | Colorado State University | 0 |
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VectorBase
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VectorBase is one of eight Bioinformatics Resource Centers funded by NIAID to provide web-based resources to scientific community conducting basic... | 1 | ||
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Vertebrate Bridging Ontology (VBO)
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An ontology of homologies between anatomical structures across species within the subphylum Vertebrata | Ravensara Travillian | European Bioinformatics Institute | 0 |
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VIrtual Fly Brain
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A data integration hub for Drosophila neuroanatomy. Functionality includes: - Query brain regions for innervating neurons classes and 3D neuron images. - Query brain regions and neurons for expressed trangenes and phenotypes. | 1 | ||
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Virus Pathogen Resource (ViPR)
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Database and analysis resource for human pathogenic viruses, including sequence, surveillance and host response data. | Richard H. Scheuermann, et al. | J. Craig Venter Institute | 7 |
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VIVO
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VIVO is an open source semantic web application originally developed and implemented at Cornell. When installed and populated with researcher... | (see project homepage) | (see project homepage) | 2 |
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VPICU
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VPICU | CHLA | 0 | |
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Wandora
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Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical... | Grip Studios Interactive | 1 | |
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web service
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It is a healthcare analysis system | Health | 19 | |
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wFleaBase
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wFleaBase is a repository of data and an electronic information service provided for the Daphnia Genomics Consortium (DGC) and the general scientific community. | 1 | ||
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WormBase
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WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible... | 1 | ||
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XEML Interactive Designer
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XEML Lab has been created to assist plant biologists in designing and documenting simple or sophisticated experiments in a machine... | Max Planck Institute of Molecular Plant Physiology | 5 |