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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Dana-Farber Cancer Institute Resource Report Resource Website 1+ mentions |
Dana-Farber Cancer Institute (RRID:SCR_003040) | DFCI | institution |
Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world. |
child, adult human, pediatric, young human |
has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: Spotfinder is parent organization of: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is parent organization of: Gene Index Project is parent organization of: CistromeMap is parent organization of: BINOCh is parent organization of: Dana Farber Tissue Bank is parent organization of: CistromeFinder is parent organization of: TM4 is parent organization of: WorfDB is parent organization of: Predictive Networks is parent organization of: RamiGO is parent organization of: DFCI Animal Resources Facility is parent organization of: DFCI Biohazard Containment Core Facility is parent organization of: DFCI Biospecimen Repository Core Facility is parent organization of: DFCI Blais Proteomics Center is parent organization of: DFCI Clinical Research Laboratory is parent organization of: DFCI Survey and Data Management Core is parent organization of: DFCI Flow Cytometry Core Facility is parent organization of: DFCI Medical Arts Core Facility is parent organization of: DFCI Microarray Core Facility is parent organization of: Dana-Farber Cancer Institute Molecular Biology Core Facility is parent organization of: DFCI RNA Interference Screening Facility is parent organization of: DFCI Shannon McCormack Advanced Molecular Diagnostics Laboratory is parent organization of: MAnorm is parent organization of: NPS is parent organization of: DFCI Confocal and Light Microscopy Core Facility is parent organization of: DFCI Monoclonal Antibody Core Facility is parent organization of: Dana-Farber Cancer Institute Labs and Facilities is parent organization of: DFCI Center for Cancer Computational Biology is parent organization of: GeneSigDB is parent organization of: MACS is parent organization of: DGAP |
Cancer | NCI ; Jimmy Fund |
Free, Freely available | Crossref funder ID: 100007886, grid.65499.37, Wikidata: Q1159198, ISNI: 0000 0001 2106 9910, nif-0000-30432 | https://ror.org/02jzgtq86 | SCR_003040 | Dana Farber Cancer Institute, Dana-Farber | 2026-08-29 11:21:20 | 6 | ||||
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GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | data analysis software, data processing software, software application, software resource | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-08-29 11:21:46 | 1135 | |||||
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Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | authoring tool, software application, software resource | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-08-29 11:21:29 | 165 | |||||
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eDoctoring Resource Report Resource Website 1+ mentions |
eDoctoring (RRID:SCR_003336) | eDoctoring | continuing medical education, data or information resource, narrative resource, service resource, training material, training resource, training service resource | Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making | clinical, medical education, medical, clinical medicine, ethics, clinical management, epidemiology, communication, legal, social, implication, genetic testing, palliative care, end-of-life care, prostate cancer screening, decision-making, prostate cancer, medicine, tutorial, article, video, fact, training material |
has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom has parent organization: University of California; California; USA |
NCI ; NIH ; CDC ; NHGRI ; Health Resources and Services Administration ; Paul G. Allen Family Foundation ; Robert Wood Johnson Foundation |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31964 | http://edoctoring.ncl.ac.uk/System_Check/psa_detect_html;clickonRouletteWheels | SCR_003336 | 2026-08-29 11:21:52 | 1 | ||||||
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caTRIP Resource Report Resource Website 1+ mentions |
caTRIP (RRID:SCR_003409) | caTRIP | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity. | element, clinical, patient, structure, tissue, trial, tumor, common data element, clinician, data technician, java, outcomes research, ctsa | has parent organization: Cancer Biomedical Informatics Grid | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33400 | SCR_003409 | 2026-08-29 11:21:32 | 2 | |||||||
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Proteome Commons Tranche repository Resource Report Resource Website 1+ mentions |
Proteome Commons Tranche repository (RRID:SCR_003441) | Tranche | software resource | A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most. | proteome, storage, proteomics, distributed, server, mass spectrometry, protein, peptide, file sharing, security |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA has parent organization: Proteome Commons |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:21063945 PMID:20356086 |
Open unspecified license (Apache v2); registration required . See Terms of Use, Https://proteomecommons.org/terms.jsp | nif-0000-33195 | http://tranche.proteomecommons.org | SCR_003441 | Tranche Project | 2026-08-29 11:21:57 | 8 | ||||
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caTIES - Cancer Text Information Extraction System Resource Report Resource Website |
caTIES - Cancer Text Information Extraction System (RRID:SCR_003444) | caTIES | data access protocol, data processing software, software application, software resource, web service | The Cancer Text Information Extraction System (caTIES) provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations. caTIES focuses on two important challenges of bioinformatics * Information extraction (IE) from free text * Access to tissue. Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed. Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers. caTIES has three goals designed to solve these problems: * Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies to populate caBIG-compliant data structures. * Provide researchers with the ability to query, browse and create orders for annotated tissue data and physical material across a network of federated sources. With caTIES the SPR acts as a locator to tissue resources. * Pioneer research for distributed text information extraction within the context of caBIG. caTIES focuses on IE from SPRs because they represent a high-dividend target for automated analysis. There are millions of SPRs in each major hospital system, and SPRs contain important information for researchers. SPRs act as tissue locators by indicating the presence of tissue blocks, frozen tissue and other resources, and by identifying the relationship of the tissue block to significant landmarks such as tumor margins. At present, nearly all important data within SPRs are embedded within loosely-structured free-text. For these reasons, SPRs were chosen to be coded through caTIES because facilitating access to information contained in SPRs will have a powerful impact on cancer research. Once SPR information has been run through the caTIES Pipeline, the data may be queried and inspected by the researcher. The goal of this search may be to extract and analyze data or to acquire slides of tissue for further study. caTIES provides two query interfaces, a simple query dashboard and an advanced diagram query builder. Both of these interfaces are capable of NCI Metathesaurus, concept-based searching as well as string searching. Additionally, the diagram interface is capable of advanced searching functionalities. An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time. caTIES provides the following web services by default: MMTx Service, TIES Coder Service | extraction, cancer, code, de-identification, information, paraffin, pathology, research, structure, surgical, system, tissue, tool, text, natural language processing, tissue banking, translational research, data sharing, collaboration, natural language processing, text-processing, text-mining, grid computing, service oriented architecture, query visualization, medical record, bioinformatics, automated coding |
is listed by: Biositemaps is related to: Cancer Biomedical Informatics Grid has parent organization: University of Pittsburgh School of Medicine; Pennsylvania; USA |
Cancer Biomedical Informatics Grid contract 79207CBS10; NCI R01 CA132672; NCI U01 CA 091343; NCRR U54 RR023506-01 |
PMID:20442142 | Open unspecified license | nif-0000-33212 | SCR_003444 | Cancer Text Information Extraction System, Cancer Text Information Extraction System (caTIES) | 2026-08-29 11:21:57 | 0 | |||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data or information resource, data repository, database, service resource, storage service resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NCI U01 CA105417; NCRR U24 RR021760; NIAAA U01 AA014425; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIA R01 AG043930; NIDA P20 DA21131; NIGMS R01 GM123489 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-08-29 11:21:04 | 499 | |||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, atlas, data analysis service, data or information resource, data repository, database, image repository, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-08-29 11:21:13 | 14 | ||||
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OSUCCC-James Resource Report Resource Website |
OSUCCC-James (RRID:SCR_004790) | OSUCCC-James | data or information resource, international standard specification, narrative resource, portal, standard specification, topical portal | As the Midwest''s first and Ohio''s only fully dedicated cancer hospital and research institute, The Ohio State University Comprehensive Cancer CenterArthur G. James Cancer Hospital and Solove Research Institute (OSUCCC-James) is one of the nation''s premier cancer centers for the prevention, detection and treatment of cancer. The OSUCCC-James is one of only 40 centers in the United States designated by the National Cancer Institute a Comprehensive Cancer Center. In addition, the OSUCCC-James is a founding member of the National Comprehensive Cancer Network (NCCN), an alliance of 21 of the world''s leading cancer centers that develops clinical practice guidelines to improve the quality and effectiveness of care provided to patients with cancer. The Ohio State cancer program is part of The Ohio State University, the largest public university in the nation. We are affiliated with The Ohio State University Medical Center, one of the largest and most diverse academic medical centers in the nation and the only academic medical center in central Ohio. The cancer program at Ohio State encompasses more than 200 comprehensive cancer center members from 13 of the 18 colleges at The Ohio State University and includes physicians from 16 specialties. The OSUCCCJames'' singular focus on cancer has led to multiple accomplishments that have changed the standards of care with respect to prevention, diagnosis and treatment, in a way that substantially improves outcomes for cancer patients. |
is related to: OSU Nucleic Acid Shared Resource is related to: OSU Nutrient and Phytochemical Analytics Shared Resource has parent organization: Ohio State University; Ohio; USA is parent organization of: Ohio State Leukemia Tissue Bank |
NCI | nlx_78698 | SCR_004790 | Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute, OSUCCC - The James Cancer Hospital and Solove Research Institute, Ohio State University Comprehensive Cancer Center, Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Solove Research Institute, The James, The James Comprehensive Cancer Center, OSUCCC | 2026-08-29 11:22:00 | 0 | ||||||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | data or information resource, interchange format, markup language, narrative resource, standard specification | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-08-29 11:22:23 | 2 | ||||||
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Ligand Expo Resource Report Resource Website |
Ligand Expo (RRID:SCR_006636) | data or information resource, database, resource | An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. | element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS ; NIDDK |
PMID:15059838 | nif-0000-21237, OMICS_02751 | http://ligand-depot.rutgers.edu/ | SCR_006636 | Ligand Depot | 2026-08-29 11:22:46 | 0 | ||||||
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Pathway Interaction Database Resource Report Resource Website 50+ mentions |
Pathway Interaction Database (RRID:SCR_006866) | PID, NCI Nature PID | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 27, 2016. Curated database of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. All interactions are assembled into pathways, and can be accessed by performing searches for biomolecules, or processes, or by viewing predefined pathways. This was a collaborative project between the NCI and Nature Publishing Group (NPG) from 2006 until September 22nd, 2012, and is no longer being updated. PID is aimed at the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. The database focuses on the biomolecular interactions that are known or believed to take place in human cells. It can be browsed as an online encyclopedia, used to run computational analyses, or employed in ways that combine these two approaches. In addition to PID''''s predefined pathways, search results are displayed as dynamically constructed interaction networks. These features of PID render it a useful tool for both biologists and bioinformaticians. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is supplemented by a concise editorial section that includes specially written synopses of recent important research articles in areas related to cancer research, and specially commissioned Bioinformatics Primers that provide practical advice on how to make the most of other relevant online resources. The database and editorial content are updated monthly, and users can opt to receive a monthly email alert to stay informed about new content. Note: as of September 23, 2012 the PID is no longer being actively curated. NCI will maintain the PID website and data for twelve months beyond September 2012 to allow interested parties to obtain the previously curated data before the site is retired in September 2013. | cellular process, interaction, neuroscience, pathway, molecule, cancer, molecular interaction, signaling pathway, visualization, connectivity, interaction network |
is related to: BioCarta Pathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: KOBAS is related to: Reactome is related to: hiPathDB - human integrated Pathway DB with facile visualization has parent organization: National Cancer Institute |
NCI | PMID:18832364 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03286 | SCR_006866 | Pathway Interaction Database | 2026-08-29 11:22:43 | 97 | |||||
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PeptideAtlas Resource Report Resource Website 500+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | data or information resource, data repository, database, service resource, storage service resource | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-08-29 11:22:42 | 511 | ||||
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NCI Mouse Repository Resource Report Resource Website 10+ mentions |
NCI Mouse Repository (RRID:SCR_002264) | NCIMR | biomaterial supply resource, material resource, organism supplier | The NCI Mouse Repository cryoarchives and distributes strains of genetically engineered mice that are of immediate interest to the cancer research community. These are either gene-targeted or transgenic mice that display a cancer-related phenotype, or tool strains (e.g., cre transgenics) that can be used to develop new cancer models. You do not have to be a member of the NCI Mouse Repository or a recipient of NCI funding to have your mouse model distributed through the NCI Mouse Repository. NCI Mouse Repository strains are maintained as live colonies or cryoarchived as frozen embryos, depending on demand. Up to three breeder pairs may be ordered from live colonies. Cryoarchived strains are supplied as frozen embryos or recovery of live mice by the NCI Mouse Repository may be requested. | embryo, engineered, frozen, gene, genetically, breed, breeder, cancer, colony, cryoarchive, human, live, model, mouse model, phenotype, strain, transgenic, mutant, female, male |
is listed by: One Mind Biospecimen Bank Listing has parent organization: NCI-Frederick |
NCI | Free, Freely available | nif-0000-20985 | http://mouse.ncifcrf.gov/ | SCR_002264 | MMHCC, MMHCC Repository, Mouse Models of Human Cancers Consortium (MMHCC) Repository, Mouse Models of Human Cancers Consortium Repository | 2026-08-29 11:21:01 | 19 | |||||
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Macromolecular Crystallography Research Resource Resource Report Resource Website 1+ mentions |
Macromolecular Crystallography Research Resource (RRID:SCR_001442) | PXRR, PXRR at the NSLS | access service resource, analysis service resource, biomedical technology research center, production service resource, service resource, training resource | Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage. | protein crystallography, macromolecule, structure, structure determination, synchrotron x-ray diffraction, crystallography, microspectrophotometry, structural biology technology center, beamline | NCI 2P30CA023168-21 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152667 | SCR_001442 | Macromolecular Crystallography Research Resource at the NSLS, Macromolecular Crystallography Research Resource at the National Synchrotron Light Source, Research Resource for Macromolecular Crystallography at the National Synchrotron Light Source | 2026-08-29 11:20:43 | 2 | |||||||
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High-Throughput GoMiner Resource Report Resource Website 1+ mentions |
High-Throughput GoMiner (RRID:SCR_000173) | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories. | term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GoMiner has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
NCI 1Z01BC010842-01 | PMID:15998470 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149300 | SCR_000173 | 2026-08-29 11:20:20 | 2 | |||||||
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Trans-Institute Angiogenesis Research Program Resource Report Resource Website |
Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) | TARP | data or information resource, portal, resource, topical portal | Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests. | blood vessel, growth, development, target, therapeutic, vascularization, angiogenesis, lymphangiogenesis |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Institutes of Health |
Angiogenesis, Lymphangiogenesis | JDRF ; NEI ; NHLBI ; NCI ; NICHD ; NIDDK ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152866 | SCR_000384 | Trans-Institute Angiogenesis Research Program (TARP) | 2026-08-29 11:20:34 | 0 | |||||
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Pediatric Brain Tumor Consortium Resource Report Resource Website 1+ mentions |
Pediatric Brain Tumor Consortium (RRID:SCR_000658) | PBTC | consortium, data or information resource, organization portal, portal | The PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) is a multidisciplinary cooperative research organization devoted to the study of correlative tumor biology and new therapies for primary CNS tumors of childhood. PBTC's mission is to contribute rapidly and effectively to the understanding and cure of these tumors through the conduct of multi-center, multidisciplinary, innovative studies with designs and analyses based on uniformly high quality statistical science. While the primary mission of the PBTC is to identify through laboratory and clinical science superior treatment strategies for children with brain cancers, the PBTC investigators recognize their profound responsibility to meet the special needs of the children and families as they face this enormous challenge. Members are committed to working within their institutions and communities to improve support services and follow up care for these patients and their families. The PBTC's primary objective is to rapidly conduct novel phase I and II clinical evaluations of new therapeutic drugs, new biological therapies, treatment delivery technologies and radiation treatment strategies in children from infancy to 21 years of age with primary central nervous system (CNS) tumors. A second objective is to characterize reliable markers and predictors (direct or surrogate) of brain tumors' responses to new therapies. The Consortium conducts research on brain tumor specimens in the laboratory to further understand the biology of pediatric brain tumors. A third objective is to develop and coordinate innovative neuro-imaging techniques. Through the PBTC's Neuro-Imaging Center, formed in May 2000, research to evaluate new treatment response criteria and neuro-imaging methods to understand regional brain effects is in progress. These imaging techniques can also advance understanding of significant neuro-toxicity in a developing child's central nervous system. The Neuro-Imaging Center is supported in part by private sources - grants from foundations and non-profit organizations - in addition to the NCI. As an NCI funded Consortium, the Pediatric Brain Tumor Consortium (PBTC) is required to make research data available to other investigators for use in research projects. An investigator who wishes to use individual patient data from one or more of the Consortium's completed and published studies must submit in writing a description of the research project, the PBTC studies from which data are requested, the specific data requested, and a list of investigators involved with the project and their affiliated research institutions. A copy of the requesting investigator's CV must also be provided. Participating Institutions: Children's Hospital of Philadelphia, Children's National Medical Center (Washington, DC), Children's Memorial Hospital (Chicago), Duke University, National Cancer Institute, St. Jude Children's Research Hospital, Texas Children's Cancer Center, University of California at San Francisco, and University of Pittsburgh. | human, child, pediatric, brain, tumor, cancer, brain cancer, central nervous system, imaging | NCI | grid.477819.4, nlx_143885 | https://ror.org/00hj21c17 | SCR_000658 | 2026-08-29 11:20:44 | 1 | ||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NCATS UL1 TR001425; NCI T32 CA236764; NHLBI U54 HL127624; NIEHS P30 ES006096; NIGMS U01 GM120953; NIMH R01 MH107487 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-08-29 11:25:50 | 4 |
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