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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | data or information resource, ontology, controlled vocabulary | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-02-14 02:00:58 | 44 | |||||
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Repository of molecular brain neoplasia data Resource Report Resource Website 1+ mentions |
Repository of molecular brain neoplasia data (RRID:SCR_004704) | REMBRANDT | data analysis service, portal, analysis service resource, data or information resource, production service resource, service resource, topical portal, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype |
is related to: Gene Ontology is related to: Glioma Molecular Dignostic Initiatives has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI ; NINDS |
PMID:19208739 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00230 | SCR_004704 | REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) | 2026-02-14 02:00:59 | 2 | ||||
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PANTHER Resource Report Resource Website 5000+ mentions |
PANTHER (RRID:SCR_004869) | PANTHER | ontology, data analysis service, analysis service resource, data or information resource, production service resource, service resource, controlled vocabulary, database | System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | hidden markov model, human, mouse, genome, protein, gene, function, pathway, ortholog, phylogenetic tree, gene ortholog, protein family, gene function, evolution, data set, molecular function, biological process, cellular component, transcript, FASEB list |
is used by: NIF Data Federation is used by: YPED is used by: EMBRYS is related to: Gene Ontology is related to: Pathway Commons is related to: KOBAS has parent organization: University of Southern California; Los Angeles; USA is parent organization of: PANTHER Evolutionary analysis of coding SNPs |
NIGMS GM081084 | PMID:23193289 PMID:20015972 PMID:12952881 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015893, nlx_84521 | SCR_004869 | PANTHER Classification System, Protein ANalysis THrough Evolutionary Relationships Classification System, Protein ANalysis THrough Evolutionary Relationships, PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System | 2026-02-14 02:00:48 | 8331 | |||||
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GOdist Resource Report Resource Website |
GOdist (RRID:SCR_005770) | GOdist | data analysis software, software resource, data processing software, software application | GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, function, gene, gene expression, gene ontology, matlab, affymetrix, microarray, biological process, molecular function, cellular component, fisher exact test, kolmogorov-smirnov |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:15550480 | Free for academic use | nlx_149260 | SCR_005770 | 2026-02-14 02:01:00 | 0 | |||||||
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Ontologizer Resource Report Resource Website 100+ mentions |
Ontologizer (RRID:SCR_005801) | Ontologizer | data processing software, data analysis service, analysis service resource, production service resource, source code, service resource, software application, software resource | The Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods. The tool can be started directly from the web using Java webstart. For graph visualizations, users need to install the GraphViz library. The tool is freely available to all, and source code is available at SourceForge. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, biological data, gene ontology, statistical analysis, fisher exact test, visualization, graph, java, annotation, parent-child, topology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
DFG SFB 760 | PMID:18511468 PMID:17848398 |
Free for academic use | nlx_149289 | SCR_005801 | The Ontologizer | 2026-02-14 02:01:00 | 122 | |||||
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THEA - Tools for High-throughput Experiments Analysis Resource Report Resource Website |
THEA - Tools for High-throughput Experiments Analysis (RRID:SCR_005802) | THEA | data analysis software, software resource, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, analysis, ontology, microarray, genomic, annotation, gene ontology, data mining, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Virtual Biology Lab |
French Ministry of Higher Education and Research ; Bioinformatic Program |
PMID:15130932 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149290 | SCR_005802 | Tools for High-throughput Experiments Analysis | 2026-02-14 02:01:11 | 0 | |||||
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PubSearch Resource Report Resource Website 1+ mentions |
PubSearch (RRID:SCR_005830) | PubSearch | data or information resource, software resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotate, editor, literature curation tool, literature, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR has parent organization: Stanford University; Stanford; California |
NHGRI R01HG02728 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149338 | SCR_005830 | 2026-02-14 02:00:59 | 1 | |||||||
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MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | data analysis software, software resource, data processing software, software application | MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible | gene, gene ontology, gene association, gene expression, profile, microarray, pathway, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at San Francisco; California; USA has parent organization: Gene Map Annotator and Pathway Profiler |
University of California at San Francisco; California; USA ; San Francisco General Hospital; California; USA ; NHLBI ; NCRR MO1RR00083 |
PMID:12540299 | Free for academic use | nlx_149270 | SCR_005791 | 2026-02-14 02:01:11 | 26 | ||||||
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GOArray Resource Report Resource Website 1+ mentions |
GOArray (RRID:SCR_005785) | GOArray | data analysis software, software resource, data processing software, software application | GOArray is a Perl program which inputs a lists of genes annotated as of interest (GOI) or not, and determines if any associated GO terms have an overrepresentation of GOI. A permutation test is optionally used to assess confidence in the results. Output includes multiple visualizations and supplementary information and, for future reference, a summary of the statistical methods used. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, gene, visualization, gene ontology, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Yale School of Medicine; Connecticut; USA |
Free for academic use | nlx_149259 | http://goarray.med.yale.edu/GOArray/ | SCR_005785 | 2026-02-14 02:01:10 | 1 | |||||||
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go-perl Resource Report Resource Website 10+ mentions |
go-perl (RRID:SCR_005730) | go-perl | software resource | go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules. go-perl comes bundled with XSL (Extensible Stylesheet Language) transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools. Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, annotation, software library, slimmer-type tool, parser |
is listed by: Gene Ontology Tools is related to: OBO is related to: go-moose is related to: go-db-perl has parent organization: Comprehensive Perl Archive Network has parent organization: Gene Ontology |
Free for academic use | nlx_149190 | SCR_005730 | 2026-02-14 02:01:00 | 10 | ||||||||
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TrED Resource Report Resource Website 1+ mentions |
TrED (RRID:SCR_005869) | TrED | data processing software, data or information resource, data analysis software, software application, software resource, database | TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. | expressed sequence tag, transcriptional profile, fungal pathogen, bmu01672, chuv862.00, mya-3108, cdna, pathway, microarray, classification, blast, unisequence, peptide, annotation |
is related to: Gene Ontology is related to: KEGG is related to: GenBank is related to: Pfam |
Ministry of Science and Technology of China 2006AA020504 | PMID:17650345 | nlx_149408 | SCR_005869 | TrED - T. rubrum Expression Database, Trichophyton rubrum Expression Database, Trichophyton rubrum Expression Database (TrED) | 2026-02-14 02:01:10 | 5 | ||||||
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BiNGO: A Biological Networks Gene Ontology tool Resource Report Resource Website 500+ mentions |
BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) | BiNGO | software resource | The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, ontology, statistical analysis, term enrichment, biological network, plugin, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:15972284 | Open unspecified license - Free for academic use | nlx_149196, biotools:bingo | https://bio.tools/bingo | SCR_005736 | Biological Networks Gene Ontology | 2026-02-14 02:01:00 | 790 | |||||
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InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | data analysis service, analysis service resource, production service resource, service resource, software resource | Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups. | protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Wurzburg; Bavaria; Germany |
PMID:24428905 | OMICS_02237 | SCR_006243 | ISAAC (Interspecies Analysing Application using Containers), ISAAC - InterSpecies Analysing Application using Containers, Interspecies Analysing Application using Containers - ISAAC | 2026-02-14 02:01:15 | 35 | |||||||
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ConceptWiki Resource Report Resource Website 1+ mentions |
ConceptWiki (RRID:SCR_006362) | ConceptWiki | narrative resource, data or information resource, people resource, wiki | A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki. | wiki, community, concept, unambiguous, repository |
is used by: Open PHACTS is related to: Gene Ontology is related to: Unified Medical Language System is related to: UniProtKB |
Public, The community can contribute to this resource | nlx_152103 | http://www.conceptwiki.org/index.php/Main%20Page | SCR_006362 | 2026-02-14 02:01:06 | 3 | |||||||
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GOCat Resource Report Resource Website 1+ mentions |
GOCat (RRID:SCR_003608) | GOCat | data analysis service, analysis service resource, production service resource, service resource, software resource | Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances. | machine learning, classification |
is related to: Gene Ontology has parent organization: University of Geneva; Geneva; Switzerland |
PMID:23842461 | nlx_157764 | SCR_003608 | GOCat the Gene Ontology Categorizer, GOCat - the Gene Ontology Categorizer | 2026-02-14 02:00:34 | 2 | |||||||
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Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | Quantitative Enrichment of Sequence Tags: QuEST | 2026-02-14 02:00:40 | 49 | ||||||
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Neural-Immune Gene Ontology Resource Report Resource Website 1+ mentions |
Neural-Immune Gene Ontology (RRID:SCR_004120) | NIGO | data or information resource, ontology, controlled vocabulary | Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains. | obo |
is listed by: BioPortal is related to: Gene Ontology |
nlx_157506 | SCR_004120 | 2026-02-14 02:00:37 | 1 | |||||||||
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MeGO Resource Report Resource Website |
MeGO (RRID:SCR_000110) | MeGO | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up. | phage, plasmid, protein family, mobile genetic element, obo |
is listed by: BioPortal is related to: OBO is related to: AmiGO is related to: Gene Ontology has parent organization: A Classification of Mobile genetic Elements |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156939 | SCR_000110 | Mobile Genetic Element Ontology | 2026-02-14 01:59:37 | 0 | |||||||
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GenNav Resource Report Resource Website 1+ mentions |
GenNav (RRID:SCR_000147) | GenNav | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. | image, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: National Library of Medicine |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149123 | SCR_000147 | 2026-02-14 01:59:38 | 1 | ||||||||
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OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-02-14 01:59:49 | 1 |
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