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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
GENCODEResource, project portal, dataset, portal, data or information resourceHuman and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.human, mouse, genome, annotation, sequence, gene featuresSCR_014966(GENCODE, RRID:SCR_014966)NHGRI, Wellcome Trustaffiliated with: ENCODEPMID:22955987Last checked down
GOtchaResource, analysis service resource, data analysis service, service resource, production service resourceGOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online toolfunction, protein, prediction, genome, annotation, gene, statistical analysisSCR_005790(GOtcha, RRID:SCR_005790)University of Dundee; Scotland; United Kingdom European Union fifth framework, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15550167Last checked downnlx_149269http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html
NEMBASEResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceNEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets.nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigeneSCR_006070(NEMBASE, RRID:SCR_006070)nematodes.org BBSRC, Hospital for Sick Children, MRC, NERC, Wellcome TrustReferences (2)Last checked downnlx_151476
OME-TIFF FormatResource, narrative resource, standard specification, data or information resourceA standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane.microscopy, format, archiving, data management, annotation, mark up, metadata standard, standard, tiff, ome-xmlSCR_002636(OME-TIFF Format, RRID:SCR_002636)OME - Open Microscopy Environment Wellcome Trustrelated to: JCB DataViewer, Cell Image Library (CIL), HMS LINCS Database, Stowers Original Data Repository, Bio-Formats, listed by: FORCE11PMID:15892875Last checked upnlx_156061
PRIDEResource, service resource, data or information resource, data repository, storage service resource, databaseCentralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomartSCR_003411(PRIDE, RRID:SCR_003411)European Bioinformatics Institute BBSRC, European Union FP7, Wellcome Trustrelated to: HUPO Proteomics Standards Initiative, ProteomeXchange, used by: ProteomeXchange, BioSample Database at EBI, listed by: Biositemaps, re3data.orgReferences (2)Last checked upnif-0000-03336
GeneDB TbruceiResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.blast, sequence, annotation, genomeSCR_004786(GeneDB Tbrucei, RRID:SCR_004786)GeneDB Wellcome Trustrelated to: AmiGO, TriTrypDB, used by: NIF Data FederationPMID:16020726Last checked upnlx_78417
Zebrafish Brain AtlasResource, reference atlas, service resource, storage service resource, atlas, image repository, data repository, data or information resourceCollates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repositorySCR_000606(Zebrafish Brain Atlas, RRID:SCR_000606)University College London; London; United Kingdom BBSRC, European Union, Wellcome Trustrecommends: Zebrafish Anatomical Ontology, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_149455http://zebrafishucl.org/
TriTrypDBResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).kinetoplastid parasite, pathogen, genome, gene chromosome, annotation, trypanosomatidae, parasite, blastSCR_007043(TriTrypDB, RRID:SCR_007043)Eukaryotic Pathogen Database Resources (EuPathDB) Bill and Melinda Gates Foundation, Wellcome Trustrelated to: GeneDB, GeneDB Lmajor, GeneDB TbruceiPMID:19843604Last checked upnlx_152064
CellMLResource, narrative resource, interchange format, markup language, standard specification, data or information resourceThe CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.biological model, cell, mathematical model, mathematics, metadata, model structure, model, xml, annotation, mark up languageSCR_008061(CellML, RRID:SCR_008061)University of Auckland; Auckland; New Zealand aneurIST, Foundation for Research Science and Technology, International Union of Physiological Sciences: Physiome Project, Maurice Wilkins Centre for Molecular Biodiscovery, NZIMA, VPH NoE, Wellcome Trustrelated to: PathGuide: the pathway resource list, listed by: 3DVCReferences (7)Last checked upnif-0000-10448
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