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An collaborative tool which allows users to edit LaTeX documents in their browser. Multiple users can simultaneously access and edit the same LaTeX document and see the changes in real time. The latest version is available online, and the built in chat helps communicate with others while editing.
Proper citation: ShareLaTeX (RRID:SCR_002652) Copy
http://bioportal.bioontology.org/
Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.
Proper citation: BioPortal (RRID:SCR_002713) Copy
A prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. It consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology, and programs to perform hypothesis design and evaluation. There are five key components involved in making HyBrow work. # The Event-based ontology for representing biological knowledge # The Discreet Event Systems based conceptual framework which provides the theory that allows us to make statements in a context free formal language (made up of the ontology) and evaluate the statements for validity using constraints declared on existing data # The rule library that provides the steps to apply those constraints and decide support, contradiction or no comment. # The relational database that stores existing information structured into the ontology. # The user interface.
Proper citation: HyBrow (Hypothesis Browser) (RRID:SCR_006272) Copy
https://bmir-gforge.stanford.edu/gf/project/odie
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. A software toolkit to code document sets with ontologies or to enrich existing ontologies with new concepts from the document set. It contains algorithms for Named Entity Recognition, Co-reference resolution, concept discovery, discourse reasoning and attribute value extraction. The project aimed to develop a toolkit that will provide the following functionality: * Build text processing pipelines that use ontologies to annotate documents. * Enrich ontologies with new concepts that are automatically discovered in documents. * Populate an information model automatically from information extracted from documents. ODIE is open source software released under the LGPL v3.0 License. ODIE is written in Java and uses the Eclipse RCP Framework for the UI. The source code is organized into Eclipse projects.
Proper citation: Ontology Development and Information Extraction (RRID:SCR_003405) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
