Curator Dashboard

Program to map biomedical text to the UMLS Metathesaurus and to discover Metathesaurus concepts referred to in text based on symbolic, natural-language processing and computational-linguistic techniques.

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• RRID-Legacy
• 10 years ago - submitted by Anita Bandrowski

Group that provides open source, college-level textbooks to instructors and their students. Educators can use the textbooks in class and access faculty-specific resources and content online.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Set of shared application programming interface specifications for interoperable functionality in digital image repositories. It utilizes JSON-LD, linked data, and standard W3C web protocols to parse and share digital image data, migrate across technology systems, and provide enhanced image access.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Modular, web-based bioinformatics system for research studies and clinical trials data collection. Tools include a data dictionary, data repository, meta study, global unique identifiers for studies, protocol management and data capture, and query and exportation of data.

• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 10 years ago - by Anonymous

Module of SOAPdenovo2 commonly used independently to close gaps in genome assemblies.

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• SciCrunch
• 10 years ago - by Anonymous

Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status.

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• SciCrunch
• 10 years ago - by Anonymous

Semi-automatic crystallographic data collection software that integrates data collection, data reduction, phasing and model building in a single software package.

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• RRID-Legacy
• 10 years ago - by Anonymous

Web based data analysis tool for microbiome statistical analysis, visual explortation, and data integration. It supports compositional profiling, functional profiling, comparative analysis, and meta analysis of microbiome datasets.

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• dkNET
• 10 years ago - submitted by Ko-Wei Lin

Server that contains a registry of text mining tools primarily within the biomedical field. It includes resources for biomedical text annotation visualization, biomedical text annotation prediction, and benchmarking biomedical entity recognition between independent automatic prediction systems.

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• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Question answering platform for integration of various Natural Language Processing tasks for the biomedical domain. It is built on top of the SAP HANA database and uses MeSH to navigate sentences extracted from papers. Olelo processes three types of questions based on the type of answer a user desires. Answers can be returned as MeSH ontological terms, short answers or facts, and summaries. Document abstracts associated with the search topic are also available for reference.

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• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Text mining tool for publishers and researchers. UNSILO modules possess functions such as searching, recommending articles with similar topics, mapping article relationships, and providing insights into article trends and metrics.

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• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Software semantic platform for curating and searching figures. Allows to share scientific figures and underlying data in way that is machine readable and findable. Platform for researchers and publishers to make their papers discoverable based on their data content. Used to make scientific papers discoverable based on data content, to enable researchers to find specific data, to test or generate new hypotheses, and to share and connect data. Openly accessible and easily applicable data discovery tool as initiative by EMBO.

• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Search engine that mines life sciences papers using Natural Language Processing and Machine Learning to clean, tag and structure the data. Insights focus on experimentation and include objective recommendations, ratings and insights for reagents, lab equipment, assays, protocols and researchers.

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• SciCrunch
• 10 years ago - by Anonymous

Text mining tool that finds similarity between documents based on sentences and tokens such as ontology terms, instead of simple similarity based on lexical terms.

• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Text mining tool from Europe PMC that allows biological terms or concepts to be highlighted for readers on full text articles. These terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. However, it is up to the reader to control which selection of highlighted concepts they see. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model and stored in a triple store via the EMBL-EBI RDF Platform. As a reader views an article in a web browser, any annotations in the triple store associated with the article are made available in a menu alongside the article.

• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Text mining consortium and hub for code and resources. Its ultimate goal is to create an infrastructure that encourages the use, incorporation, and interoperability of existing text mining technologies in scientific publications.

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• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Cross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select databases.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Framework for creating 3D neuronal morphologies from point/diameter descriptions.

• RRID-Legacy
• 10 years ago - submitted by David Kennedy

Information portal for practicing endocrinology physicians, trainees, fellows, and other health professionals. Essentially a regularly updated web textbook, it contains endocrinological information written by physicians for other practicing endocrinologists.

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• dkNET
• 10 years ago - submitted by Ko-Wei Lin