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DataMed
Helps researchers to find data of interest in a broad spectrum of high quality repositories. DataMed is designed to be, for data, what PubMed has been for the scientific literature. DataMed stores metadata generic enough to describe any dataset using a model called Data Tag Suite. DataMed is intended to point to data of interest by indicating the repository in which it is found, and providing some minimal information about the data so users can elect to follow the links to those repositories or move on to the next entry.
BARCdb / Biobanking Analysis Resource Catalogue
A freely available web resource, listing expertise and molecular resource capabilities of research centres and biotechnology companies. The database is designed for researchers who require information on how to make best use of valuable biospecimens from biobanks and other sample collections, focusing on the choice of analytical techniques and the demands they make on the type of samples, pre-analytical sample preparation and amounts needed.
dkNET / National Institute of Diabetes and Digestive and Kidney Diseases Information Network
An information network launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources, as data, software tools, materials, services, projects and organizations. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. dkNET provides an ideal environment for illustrating some of the opportunities and challenges associated with organizing and searching the new types of digital research objects, including dynamic databases, produced in support of biomedical research.
DESTAF / Dragon Exploration System for Toxicants and Fertility
A specialized, public resource specifically aimed at researchers investigating reproductive toxicity. Its primary goal is to enable researchers to efficiently and rapidly query the human reproductive toxicity literature in an innovative manner and on a deeper level than articles and from differing gene/protein-, protein-, metabolite / enzyme-, biological- and chemical/toxin-, disease- and human anatomical-centric perspectives.
LIDPD / Levodopa-Induced Dyskinesia in Parkinson's Disease
Summarizes literature-curated information on levodopa-induced dyskinesia (LID) genetics. LIPDP is a publicly available web resource that investigates the LID-associated genes in a broader functional context through analysis of their relationships based on network models. It uses different underlying networks and allows to incorporate data into the analyses. The core of LIDPD is a set of Panel genes that have been associated with LID in the scientific literature. Different Highlight datasets provide additional gene annotations or associations with Parkinson's disease.
IARP / International Aging Research Portfolio
An online database to centralize aging research projects across numerous research disciplines. IARP integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research.
BioM2MetDisease
Collects experimental supported associations between biomolecules (miRNAs, metabolites, small molecules/drugs) and metabolic diseases. BioM2MetDisease provides detailed information including biomolecule and metabolic disease names, species, experimental techniques, experimental tissue, dysregulation patterns, etc. to describe how a biomolecule is related to metabolic disease. It also offers PubChem Compound Identifier (CID) for metabolites and small molecules/drugs, miRBase accession for miRNAs, Disease Ontology (DO) identifier and International Classification of Diseases (ICD-10) for metabolic diseases.
RegenBase
A knowledge base of spinal cord injury (SCI) biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources.
PatSeq Data
Compiles data about patents disclosing genetic sequences. PatSeq Data is built around data collected from national patent offices, public sequence listings repositories or intellectual property organizations. Searches can be made by jurisdiction, document type, sequence type or location. The database provides additional statistics based on criteria, such as document or sequence type or data sources, as well as information about the public availability of sequences listings in the corresponding patent office. It is part of the PatSeq toolkit.
Manually annotated miRNA-disease and miRNA-gene interaction Corpora
Permits to extract automatically mentions of miRNAs, species, genes/proteins, disease and relations from scientific literature. This tool manually annotated is able to two types of miRNA mentions namely Specific (with numerical identifiers) and Non-Specific (without numerical identifiers). It uses information about miRNAs and miRNA-relations based on published scientific literature. This tool provides the basis for building a knowledge-based approach to model regulatory network for identification of deregulated miRNAs and genes/proteins.
PGC DB / Psychiatric Genomics Consortium DataBase
Contains the full results from all published PGC studies. The results files of the PGC Database are available below along with the LD pruned version suitable for polygenic profile scoring. The purpose of the Psychiatric Genomics Consortium (PGC) is to unite investigators around the world to conduct meta- and mega-analyses of genome-wide genomic data for psychiatric disorders. The PGC includes over 800 investigators from 38 countries, it represents the largest consortium and the largest biological experiment in the history of psychiatry.
Cellosaurus
Provides information about cell lines. Cellosaurus is composed of immortalized cell lines, naturally immortal cell lines, finite life cell lines when those are distributed and used widely, vertebrate cell line with an emphasis on human, mouse and rat cell lines, and invertebrate cell lines. It contains more than 100 000 cell lines, representing over 550 species. The database furnishes data such as synonyms, cross-references and references to publications, databases or ontologies.
BRD / Biospecimen Research Database
Accommodates Standard Operating Procedures (SOP). BRD contains peer-reviewed primary and review articles as well as SOPs in the field of human Biospecimen Science. It is organized in a hierarchy system consisting of two tiers: (1) SOPs, established protocols; and (2) Biospecimen Evidence-based Practices (BEBP), procedural guidelines developed using literature evidence. The database is searchable by keywords or by curated files like: source organization, tier, applicable biospecimens, and topic.
DeTEXT / Database for Extracting TEXT
Obsolete
Assists users in assessing text extraction from biomedical literature figures. DeTEXT contains over 500 typical biomedical literature figures existing in about 300 full-text articles randomly chosen from PubMed Central. The database provides annotation guidelines, tools and makes available to users text detection and word recognition evaluation protocols. It constitutes an image dataset for biomedical literature figure detection, recognition, and retrieval that can be used as a benchmark dataset.
PAHKB / Pulmonary Arterial Hypertension KnowledgeBase
Obsolete
Records core pulmonary hypertension (PH)-related genes. PAHKB is a literature-based PAH genetic resource that contains about 340 human PH-related genes (coding and non-coding genes) curated from over one thousand PubMed abstracts. It also identifies critical signaling pathways that may be relevant to pulmonary arterial hypertension (PAH) pathogenesis The database provides users with a text query, sequence search, gene ranking, browsing using functional analysis results, highlighted pathway map, and curated mouse model.
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