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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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North Texas Traumatic Brain Injury Model System Resource Report Resource Website |
North Texas Traumatic Brain Injury Model System (RRID:SCR_005879) | NT-TBIMS | data or information resource, portal, topical portal | The 16 affiliated Model System centers throughout the United States are responsible for gathering and submitting the core data set to the national database as well as conducting research studies on traumatic brain injury (TBI) both in collaboration with the other centers and within our own site. Through our research we hope to learn more about TBI and about the issues and concerns of people with TBI. Our goals are to improve the outcome and quality of life for people who have had brain injuries and for those who are caring for the person with a TBI. The North Texas Traumatic Brain Injury Model System (NT-TBIMS) pools the efforts and talents of individuals from the Departments of Neurosurgery, Neurology, Physical Medicine and Rehabilitation, Psychiatry (Neuropsychiatry), and Neuroradiology of the two leading medical institutions in the North Texas region. To be a patient involved in the research being conducted by the North Texas Traumatic Brain Injury Model System you must have suffered a TBI, be at least 16 years of age, have received initial treatment for the TBI at either Parkland Health and Hospital System or Baylor University Medical Center and then have received rehabilitative care at either Parkland, University Hospital Zale-Lipshy, or Baylor Institute for Rehabilitation. The patient must also be able to understand and sign an informed consent to participate or, if unable, have a family member or a legal guardian who understands the form sign the informed consent for the patient. | brain injury, brain, injury, traumatic brain injury, clinical, research | has parent organization: University of Texas Southwestern Medical Center; Texas; USA | Traumatic Brain Injury | National Institute on Disability and Rehabilitation Research H133A070027 | nlx_149440 | SCR_005879 | North Texas TBI Model System, North Texas Traumatic Brain Injury Model System (NT-TBIMS) | 2026-09-19 12:51:01 | 0 | ||||||
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Universal Numerical Fingerprint Resource Report Resource Website |
Universal Numerical Fingerprint (RRID:SCR_005912) | UNF | data or information resource, narrative resource, standard specification | Citation standard that offers proper recognition to authors as well as permanent identification through the use of global, persistent identifiers in place of URLs, which can change frequently. Use of universal numerical fingerprints (UNFs) guarantees to the scholarly community that future researchers will be able to verify that data retrieved is identical to that used in a publication decades earlier, even if it has changed storage media, operating systems, hardware, and statistical program format. | identifier, universal numerical fingerprint, data citation |
is listed by: FORCE11 has parent organization: Dataverse Network Project |
nlx_149488 | SCR_005912 | Standard: Universal Numerical Fingerprint, The Standard: Universal Numerical Fingerprint | 2026-09-19 12:51:01 | 0 | ||||||||
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AIDA Toolkit Resource Report Resource Website 1+ mentions |
AIDA Toolkit (RRID:SCR_005914) | data access protocol, software resource, software toolkit, web service | A generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning. | software toolkit, web service, search, learning, storage, workflow, text indexing, text statistics, metadata storage, metadata querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, model learning | is related to: Taverna | Open source, Available as a web service, Available for download | nlx_149497 | http://adaptivedisclosure.org/aida/ | SCR_005914 | Adaptive Information Disclosure Application Toolkit | 2026-09-19 12:51:01 | 1 | |||||||
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Icahn School of Medicine at Mount Sinai; New York; USA Resource Report Resource Website 10+ mentions |
Icahn School of Medicine at Mount Sinai; New York; USA (RRID:SCR_005793) | ISMMS, MSSM | university | Icahn School of Medicine at Mount Sinai, formerly Mount Sinai School of Medicine, is graduate medical school in Manhattan, New York City. Leader in medical and scientific training and education, biomedical research and patient care. | medicine, medical, school, university, doctorate, phd |
uses: Scizzle is affiliated with: BioJupies is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: proMODMatcher is parent organization of: Enrichr is parent organization of: Neuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo Diagnostics is parent organization of: NeuronStudio is parent organization of: Rayburst Open-Source Code is parent organization of: Volume Integration and Alignment System is parent organization of: Volume Integration and Alignment System Source Code is parent organization of: NeuroGL is parent organization of: TIFF Stack Sub-Sampler is parent organization of: Cre-X-Mice: A Database of Cre Transgenic Lines is parent organization of: Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory is parent organization of: Mount Sinai Biobank is parent organization of: ChEA is parent organization of: Kismeth is parent organization of: Lists2Networks is parent organization of: Mount Sianai Department of Neuroscience is parent organization of: NetworKIN is parent organization of: Mount Sinai Alzheimer's Disease Research Center is parent organization of: Manhattan HIV Brain Bank is parent organization of: Computational Neurobiology and Imaging Center is parent organization of: L1000 Characteristic Direction Signature Search Engine is parent organization of: L1000 Fireworks Display is parent organization of: Drug Gene Budger is parent organization of: COVID-19 Crowd Generated Gene and Drug Set Library is parent organization of: GeneOverlap is parent organization of: Datanator is parent organization of: BioSimulations is parent organization of: DE-Sim is parent organization of: Appyters is parent organization of: ezTrack project is parent organization of: Minian is parent organization of: TargetRanger is parent organization of: GeneRanger is parent organization of: Kinase Enrichment Analysis 3 is parent organization of: X2K Web is parent organization of: Diabetes Data and Hypothesis Hub is parent organization of: Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Transgenic and Genome Editing Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Metabolomics Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility is parent organization of: Icahn School of Medicine at Mount Sinai RNA Nanocore Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Biorepository and Pathology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Mount Sinai Cryo-EM CoRE Core Facility |
nlx_55912, grid.59734.3c, Crossref funder ID:100007277, ISNI:0000 0001 0670 2351, Wikidata:Q1950740 | https://ror.org/04a9tmd77 | SCR_005793 | Mount Sinai School of Medicine, Icahn School of Medicine, Icahn School of Medicine at Mount Sinai | 2026-09-19 12:50:59 | 12 | |||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-09-19 12:51:00 | 7512 | |||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-09-19 12:51:00 | 8 | |||||||
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SPLINTER Resource Report Resource Website 10+ mentions |
SPLINTER (RRID:SCR_005826) | SPLINTER | software resource | Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples. |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
Cancer | Free for academic / non-profit use, Commercial use requires license | OMICS_00100 | SCR_005826 | Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion | 2026-09-19 12:51:00 | 13 | |||||||
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UM-BBD Resource Report Resource Website 1+ mentions |
UM-BBD (RRID:SCR_005787) | UM-BBD, UM-BBD enzymeID, UM-BBD pathwayID, UM-BBD reactionID, UM-BBD ruleID | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2014. Database containing information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Its goal is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students. In addition to reactions and pathways, this database also contains Biochemical Periodic Tables and a Pathway Prediction System. * Search the UM-BBD for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. * Go to Pathways and Metapathways in the UM-BBD * Lists of 203 pathways; 1400 reactions; 1296 compounds; 916 enzymes; 510 microorganism entries; 245 biotransformation rules; 50 organic functional groups; 76 reactions of naphthalene 1,2-dioxygenase; 109 reactions of toluene dioxygenase; Graphical UM-BBD Overview; and Other Graphics (Metapathway and Pathway Maps and Reaction Mechanisms). | enzyme, biocatalysis, biodegredation, chemical, pathway, reaction, microorganism, image, chemical compound, gene, enzymology | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Minnesota Supercomputing Institute ; Lhasa Limited ; University of Minnesota; Minnesota; USA ; European Union FP6 ALARM project ; NIH ; NSF 0543416; DOE DE-FG02-01ER63268; NIGMS R01GM56529; NSF 9630427 |
PMID:19767608 PMID:16381924 PMID:12519997 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03607, r3d100011317 | https://doi.org/10.17616/R33D0V | SCR_005787 | UM-BBD pathwayID, University of Minnesota Biocatalysis and Biodegradation Database, UM-BBD reactionID, Biocatalysis/Biodegradation Database, University of Minnesota Biocatalysis/Biodegradation Database, UM-BBD ruleID, Univeristy of Minnesota Biocatalysis/Biodegradation Database, UM-BBD enzymeID | 2026-09-19 12:50:59 | 9 | ||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | data or information resource, database, portal, project portal, service resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase works with: bedGraphToBigWig |
Alfred P. Sloan Foundation ; CISI ; David and Lucille Packard Foundation ; DOE ; HHMI ; NHGRI ; NIGMS GM52848; NIH ; NSF DBI 9809007; UC BIOTEuropean UnionH |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu, https://doi.org/10.17616/R3RK5C | SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-09-19 12:50:59 | 11041 | ||||||
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OMGN Resource Report Resource Website |
OMGN (RRID:SCR_005781) | OMGN | community building portal, data or information resource, portal, training resource | The Oomycete Molecular Genetics Research Collaboration Network (OMGN) is a network for research collaboration for investigators interested in oomycete molecular genetics and genomics. The goals of the OMGN is to facilitate the integration of these investigators into the community and to further strengthen the cooperative culture of this community. A particular emphasis is placed on training and integrating junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. Because of their economic impact as plant pathogens, molecular, genetic and genomics studies are well advanced in many oomycete species. These organisms have served as lead species for the entire Stramenopiles lineage, a major radiation of crown eukaryotes, distinct from plants, animals and fungi. The oomycete molecular genetics community has a strong culture of collaboration and communication, and sharing of techniques and resources. With the recent blossoming of genetic and genomic tools for oomycetes, many new investigators, from a variety of backgrounds, have become interested in oomycete molecular genetics and genomics. The proposed network is open to all researchers with an interest in oomycete molecular genetics and genomics, either at an experimental or a computational level. Investigators new to the field are always welcome, especially those interested in saprophytes and animal pathogens. Goals of OMGN # Provide training to o��mycete molecular genetics researchers, especially those from smaller institutions, in the use of bioinformatics and genomics resources. # Promote the entry, participation and training of new investigators into the field of o��mycete genomics, particularly junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. # Promote communication and collaboration, and minimize duplication of effort, within the worldwide o��mycete genomics community. # Support an O��mycete Genomics Resources Center to maintain and distribute training and research materials produced by community genomics projects. The network''s activities have been supported by two grants from the NSF Research Collaboration Networks in Biology program. | oomycete, molecular genetics, genomics, saprophyte, animal, pathogen, stramenopile | has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA | NSF EF 0130263 | nlx_149251 | SCR_005781 | OMGN - Oomycete Molecular Genetics Research Collaboration Network, Oomycete Molecular Genetics Research Collaboration Network | 2026-09-19 12:50:59 | 0 | |||||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2026-09-19 12:50:59 | 32 | ||||
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AppliChem Resource Report Resource Website 1000+ mentions |
AppliChem (RRID:SCR_005814) | commercial organization | An Antibody supplier | nlx_152277 | SCR_005814 | PanReac AppliChem, AppliChem GmbH | 2026-09-19 12:51:00 | 4849 | |||||||||||
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OWLTools Resource Report Resource Website 10+ mentions |
OWLTools (RRID:SCR_005732) | OWLTools | software resource | OWLTools (aka OWL2LS - OWL2 Life Sciences) is a java API for accessing ontologies in either OBO or OWL. OWLTools provides a bio-ontologies friendly wrapper on top of the Manchester OWL API. It provides many features, including: * convenience methods for OBO-like properties such as synonyms, textual definitions, obsoletion, replaced_by * simple graph-like operations over ontologies * visualization using the QuickGO graphs libraries Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, ontology |
is listed by: Gene Ontology Tools is related to: OBO has parent organization: Gene Ontology has parent organization: Google Project Hosting is parent organization of: OwlSim |
Open unspecified license - Free for academic use | nlx_149192 | SCR_005732 | OWL2LS - OWL2 Life Sciences, OWL Tools | 2026-09-19 12:50:58 | 18 | |||||||
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Blip: Biomedical Logic Programming Resource Report Resource Website 1+ mentions |
Blip: Biomedical Logic Programming (RRID:SCR_005733) | Blip, blipkit | software resource | Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog''''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | biology, biomedical, ontology, annotation, software library, bioinformatics, module |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects |
GNU Lesser General Public License | nlx_149193 | SCR_005733 | Blip - Biomedical Logic Programming, Biomedical Logical Programming (Blip), Biomedical Logic Programming | 2026-09-19 12:50:58 | 2 | |||||||
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Brains Matter Resource Report Resource Website |
Brains Matter (RRID:SCR_005847) | Brains Matter | data or information resource, narrative resource, podcast | Welcome to the Brains Matter podcast where brains really do matter. A discussion of science, trivia, history, and general knowledge. The show started in September 2006, and includes discussion on various topics, as well as interviews with experts in their field. You can subscribe to the show via iTunes, a standard RSS reader, or listen to the individual MP3 shows from the ''flash player'' on the website, or direct download. | brain, science | Copyright under the Creative Commons licence where appropriate, Except where otherwise specified. | nlx_149376 | SCR_005847 | Brains Matter - The Podcast on Science Curiosities and General Knowledge. Brains Really Do Matter! | 2026-09-19 12:51:00 | 0 | ||||||||
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Brain Networks Resource Report Resource Website 1+ mentions |
Brain Networks (RRID:SCR_005841) | Brain Networks | data analysis software, data processing software, software application, software resource, source code | Brain Networks: Code to perform network analysis on brain imaging data. | brain, imaging, network analysis, brain imaging, neuroimaging | has parent organization: SourceForge | PMID:21031030 | Open unspecified license - GNU General Public License (GPL) | nlx_149364 | SCR_005841 | brainnetworks | 2026-09-19 12:51:00 | 1 | ||||||
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Cell Line Ontology Resource Report Resource Website 1+ mentions |
Cell Line Ontology (RRID:SCR_005840) | CLO | controlled vocabulary, data or information resource, ontology | A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan. | cell line, owl, ontology, standardization, information integration |
is listed by: BioPortal is listed by: OBO is related to: Cell Line Knowledge Base has parent organization: University of Michigan Medical School; Michigan; USA |
The community can contribute to this resource | nlx_149363 | http://bioportal.bioontology.org/ontologies/1245, http://purl.obolibrary.org/obo/clo.owl | SCR_005840 | 2026-09-19 12:51:00 | 2 | |||||||
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University of Neuchatel; Neuchatel; Switzerland Resource Report Resource Website |
University of Neuchatel; Neuchatel; Switzerland (RRID:SCR_005875) | UniNE | university | French-speaking university based in Neuchâtel, Switzerland. The university has four faculties and more than a dozen institutes, including arts and human sciences, natural sciences, law and economics. | is related to: Pharma-Planta Consortium | grid.10711.36, nlx_158304, ISNI:0000 0001 2297 7718, Crossref funder ID:501100005353, Wikidata:Q541548 | https://ror.org/00vasag41 | SCR_005875 | University of Neuchatel, Universite de Neuchatel, University of Neuch�tel, Universit� de Neuch�tel | 2026-09-19 12:51:00 | 0 | ||||||||
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American Cancer Society Resource Report Resource Website 500+ mentions |
American Cancer Society (RRID:SCR_005756) | ACS | non profit organization | The American Cancer Society is the nationwide, community-based, voluntary health organization dedicated to eliminating cancer as a major health problem by preventing cancer, saving lives, and diminishing suffering from cancer, through research, education, advocacy, and service. Together with our millions of supporters, the American Cancer Society (ACS) saves lives and creates a world with less cancer and more birthdays by helping people stay well, helping people get well, by finding cures, and by fighting back. Headquartered in Atlanta, Georgia, the ACS has 12 chartered Divisions, more than 900 local offices nationwide, and a presence in more than 5,100 communities. | cancer, breast cancer, colon, lung, prostate, skin, breast | Cancer | grid.422418.9, Wikidata: Q463665, nlx_149219, ISNI: 0000 0004 0371 6485, Crossref funder ID: 100000048 | https://ror.org/02e463172 | SCR_005756 | American Cancer Society - The Official Sponsor of Birthdays | 2026-09-19 12:50:59 | 527 | |||||||
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ccPDB - Compilation and Creation of datasets from PDB Resource Report Resource Website 1+ mentions |
ccPDB - Compilation and Creation of datasets from PDB (RRID:SCR_005870) | ccPDB | data access protocol, data or information resource, database, software resource, web service | ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible. | secondary structure, nucleic acid interaction, ligand interaction, structure, nucleic acid, interaction, ligand, data set, function, protein, annotate, tight-turn, nucleotide interacting residue, metals interacting residue, dna/rna binding residue, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Institute of Microbial Technology; Chandigarh; India |
OSDD ; DBT ; Council of Scientific and Industrial Research; New Delhi; India |
PMID:22139939 | biotools:ccpdb, nlx_149416 | https://bio.tools/ccpdb | SCR_005870 | Compilation and Creation of datasets from PDB, ccPDB - Compilation Creation of datasets from PDB | 2026-09-19 12:51:00 | 2 |
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