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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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AD Clinical Trials Database Resource Report Resource Website |
AD Clinical Trials Database (RRID:SCR_005863) | clinical database, data or information resource, database | A database of Alzheimer's disease and dementia clinical trials currently in progress at centers throughout the U.S. | alzheimer's disease, cause, clinical trial, cure, dementia, treatment, database, clinical database | has parent organization: Alzheimer's Disease Education and Referral Center | Aging | Public | nif-0000-10344 | SCR_005863 | 2026-09-12 12:56:32 | 0 | ||||||||
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University of Louisiana; Louisiana; USA Resource Report Resource Website |
University of Louisiana; Louisiana; USA (RRID:SCR_005743) | university | Public research university in Lafayette, Louisiana. It has the largest enrollment within the nine-campus University of Louisiana System and the second largest enrollment in Louisiana. | is parent organization of: New Iberia Research Center | Wikidata:Q116485, grid.266621.7, Crossref funder ID:100008520, ISNI:0000 0000 9831 5270, nlx_12312 | https://ror.org/01x8rc503 | SCR_005743 | 2026-09-12 12:56:30 | 0 | ||||||||||
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Andrew W. Mellon Foundation Resource Report Resource Website 10+ mentions |
Andrew W. Mellon Foundation (RRID:SCR_005864) | Andrew W. Mellon Foundation | funding resource | The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results. | grant, higher education, scholarship, scholarly communication, information technology, art history, conservation, museum, performing arts, environment | nlx_149404 | SCR_005864 | 2026-09-12 12:56:32 | 13 | ||||||||||
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SIMILE Resource Report Resource Website 1+ mentions |
SIMILE (RRID:SCR_005862) | SIMILE | data or information resource, portal, topical portal | SIMILE, a joint project conducted by the MIT Libraries and MIT CSAIL, was focused on developing robust, open source tools that empower users to access, manage, visualize and reuse digital assets. SIMILE seeks to enhance interoperability among digital assets, schemata/vocabularies/ontologies, metadata, and services. A key challenge is that the collections which must inter-operate are often distributed across individual, community, and institutional stores. We seek to be able to provide end-user services by drawing upon the assets, schemata/vocabularies/ontologies, and metadata held in such stores. SIMILE will leverage and extend DSpace, enhancing its support for arbitrary schemata and metadata, primarily though the application of RDF and semantic web techniques. The project also aims to implement a digital asset dissemination architecture based upon web standards. The dissemination architecture will provide a mechanism to add useful views to a particular digital artifact (i.e. asset, schema, or metadata instance), and bind those views to consuming services. To guide the SIMILE effort we will focus on well-defined, real-world use cases in the libraries domain. Since parallel work is underway to deploy DSpace at a number of leading research libraries, we hope that such an approach will lead to a powerful deployment channel through which the utility and readiness of semantic web tools and techniques can be compellingly demonstrated in a visible and global community. The SIMILE Project and its members are fully committed to the open source principles of software distribution and open development and for this reason, it releases the created intellectual property (both software and reports) under a BSD-style license. The SIMILE Project Team Members gladly welcome community efforts. | semantic, interoperability, metadata, information |
is related to: DSpace has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Andrew W. Mellon Foundation | Open unspecified license - BSD-style license | nlx_149403 | SCR_005862 | Semantic Interoperability of Metadata and Information in unLike Environments, SIMILE Project | 2026-09-12 12:56:32 | 3 | ||||||
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CLENCH Resource Report Resource Website 1+ mentions |
CLENCH (RRID:SCR_005735) | CLENCH | data processing software, software application, software resource, source code | Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible, | gene, microarray, function, functional categorization, statistical analysis, slimmer-type tool, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: TAIR has parent organization: Stanford Center for Biomedical Informatics Research |
PMID:14764555 | Free for academic use | nlx_149216 | http://www.personal.psu.edu/nhs109/Clench | SCR_005735 | CLENCH - Cluster Enrichment, CLENCH: A program for calculating cluster enrichment using the Gene Ontology, Cluster Enrichment, Cluster Enrichment (CLENCH) | 2026-09-12 12:56:30 | 4 | |||||
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SBUR - Society for Basic Urologic Research Resource Report Resource Website |
SBUR - Society for Basic Urologic Research (RRID:SCR_005856) | SBUR | community building portal, data or information resource, funding resource, meeting resource, portal, topical portal, training resource | The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association | urology, prostate, bladder, kidney, testis, penis, award | is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology | Urologic disease, Urologic cancer, Neuro-urologic disease, Infertility, Erectile dysfunction | nlx_149393 | SCR_005856 | Society for Basic Urologic Research (SBUR), Society for Basic Urologic Research | 2026-09-12 12:56:32 | 0 | |||||||
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American Urological Association Resource Report Resource Website 100+ mentions |
American Urological Association (RRID:SCR_005859) | AUA | institution | The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy. | urology, research |
is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is parent organization of: AmerUrological's channel - YouTube |
Urologic disease | grid.422576.0, ISNI: 0000 0001 2222 2235, Wikidata: Q4745327, Crossref funder ID: 100006280, nlx_149398 | https://ror.org/00sbaqa70 | SCR_005859 | American Urological Association (AUA) | 2026-09-12 12:56:32 | 270 | ||||||
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DRCAT Resource Catalogue Resource Report Resource Website 1+ mentions |
DRCAT Resource Catalogue (RRID:SCR_005931) | DRCAT | catalog, data or information resource, database | Data resource catalog that collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. An entry includes information such as resource identifier(s), name, description and URL. ''''Query'''' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL). DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including ''''Query'''' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts. | metadata, bioinformatics, database, ontology, taxonomy, registry, annotation, data set |
is related to: EDAM Ontology has parent organization: European Bioinformatics Institute |
Acknowledgement required, See license | nlx_151280 | SCR_005931 | DRCAT (the data resource catalogue), DRCAT Resource Catalogue - Bioinformatics Web-based Data Resources, Data Resource Catalogue | 2026-09-12 12:56:33 | 2 | |||||||
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FAIRSharing Catalogue of Standards Resource Report Resource Website 1+ mentions |
FAIRSharing Catalogue of Standards (RRID:SCR_005926) | Catalogue of Standards | data or information resource, database, narrative resource, registry, standard specification | Catalogue to: 1, centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards; 2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them; 3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems. Research community, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated. Similar trends in both the regulatory arena and commercial science. The BioSharing catalogue classifies standards into three types: * reporting requirements (minimal information checklists to report of the same core set of information) * terminological artifacts (such as controlled vocabularies and ontologies to describe the information) * exchange formats (to communicate the information) You can sort columns and browse the reporting guidelines content, or you can view all the standards, or reporting guidelines, or terminological artifacts or exchange formats only. Contribute and help build the catalogue. | report guideline, exchange format, terminology artifact, terminology, metadata standard, ontology, registry, interoperability, markup |
is listed by: FORCE11 has parent organization: FAIRsharing |
BioMed Central | Creative Commons Attribution License, v3 Unported, The community can contribute to this resource | nlx_149630 | http://www.force11.org/node/4699 | http://www.biosharing.org/standards | SCR_005926 | Catalogue of Domain-specific Data Standards, Catalog of Standards, BioSharing Catalogue of Standards, BioSharing catalogue | 2026-09-12 12:56:33 | 2 | ||||
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LHP LHDL Resource Report Resource Website |
LHP LHDL (RRID:SCR_005928) | LHP, LHDL | data or information resource, simulation software, software application, software resource | Distributed repository of anatomo-functional data and of simulation algorithms, fully integrated into a seamless simulation environment and directly accessible. This infrastructure will be used to create the physiome of the human musculo-skeletal system. | algorithm, anatomo-functional data, human, musculo-skeletal, physiome, repository, simulation, system, training tools | is listed by: 3DVC | European Union | nif-0000-10464 | SCR_005928 | The Living Human Digital Library, The Living Human Project | 2026-09-12 12:56:33 | 0 | |||||||
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Dictyostelium Anatomy Ontology Resource Report Resource Website 1+ mentions |
Dictyostelium Anatomy Ontology (RRID:SCR_005929) | controlled vocabulary, data or information resource, ontology | An ontology to describe Dictyostelium where the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle is defined. There are two main goals for this new tool: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes (already in use), and in the future, of gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning. To this end, all terms are defined. The complete ontology can be browsed using EBI''s ontology browser tool. (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DDANAT) | stricture, cell type, life cycle, phenotype, gene expression | has parent organization: Dictyostelium discoideum genome database | Wellcome Trust ; NIGMS GM64426; NHGRI HG00022 |
PMID:18366659 | nlx_14988 | SCR_005929 | 2026-09-12 12:56:33 | 1 | ||||||||
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caArray Resource Report Resource Website 10+ mentions |
caArray (RRID:SCR_006053) | caArray | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management. | microarray, gene expression, data sharing, service resource, data management, annotation, interoperability, life sciences |
is listed by: re3data.org is listed by: OMICtools is related to: Cancer Biomedical Informatics Grid is related to: MAGE-TAB has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151452, OMICS_00864, r3d100010573 | https://doi.org/10.17616/R33G76 | SCR_006053 | caArray - Array Data Management System, caArray Data Portal | 2026-09-12 12:56:34 | 35 | |||||
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Read Codes Clinical Terms Version 3 Resource Report Resource Website 1+ mentions |
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) | RCD | controlled vocabulary, data or information resource, ontology | Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre | umls | is listed by: BioPortal | nlx_157570 | SCR_006055 | Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) | 2026-09-12 12:56:34 | 1 | ||||||||
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Genome Research Foundation Resource Report Resource Website 1+ mentions |
Genome Research Foundation (RRID:SCR_006056) | GRF, GF | institution | The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project | bioinformatics, genomics, genome, genome sequencing, personalized medicine, personal genomics, angiogenesis, drug, rna expression, protein structure |
has parent organization: Korean Ministry of Education Science and Technology is parent organization of: MetaBase |
Content is available under BioLicense: the freest license. | grid.410888.d, nlx_151458, Wikidata: Q5533483 | https://ror.org/03khjyh83 | SCR_006056 | Genome Foundation | 2026-09-12 12:56:34 | 1 | ||||||
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OCDM - Ontology of Craniofacial Development and Malformation Resource Report Resource Website 1+ mentions |
OCDM - Ontology of Craniofacial Development and Malformation (RRID:SCR_005999) | OCDM | controlled vocabulary, data or information resource, ontology | To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language. | craniofacial development, malformation, craniofacial malformation, anatomy | has parent organization: FaceBase | nlx_151377 | SCR_005999 | Ontology of Craniofacial Development Malformation (OCDM), Ontology of Craniofacial Development and Malformation (OCDM), OCDM - Ontology of Craniofacial Development Malformation | 2026-09-12 12:56:34 | 1 | ||||||||
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University of Michigan Department of Neuroscience Graduate Program Resource Report Resource Website 1+ mentions |
University of Michigan Department of Neuroscience Graduate Program (RRID:SCR_006002) | U-M Neuroscience Graduate Program | data or information resource, department portal, graduate program resource, organization portal, portal | The Graduate Program at the University of Michigan was constituted in 1971, making it the longest-standing neuroscience graduate program in the United States. We are a collegial and interactive group of 75 students and 115 faculty that perform research across the breadth of the neuroscience field. Neuroscience graduate students on this campus form a cohesive group, which promotes interactions among the faculty, making the Graduate Program the nexus of the neuroscience community. Graduates receive a Ph.D. in Neuroscience, which provides tremendous flexibility in choosing one's career path. There are more than 100 alumni of our Program, and these graduates work in academic research, industrial research and development, academic medicine and biotechnology. Our program captures the excitement and interaction intrinsic to the field of neuroscience. Students can seek admission to the Neuroscience Program by three different routes direct application to the Neuroscience Program, application via the Program in Biomedical Sciences and application via the Medical Scientist Training Program. | has parent organization: University of Michigan; Ann Arbor; USA | nif-0000-02211 | SCR_006002 | University of Michigan Neuroscience Graduate Program | 2026-09-12 12:56:34 | 1 | |||||||||
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Voronoia Resource Report Resource Website 10+ mentions |
Voronoia (RRID:SCR_006005) | data or information resource, database, software resource, software toolkit | Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins. | has parent organization: University Medicine Berlin; Berlin; Germany | nif-0000-03641 | http://141.42.202.21/voronoia/index.php | SCR_006005 | Voronoia | 2026-09-12 12:56:34 | 10 | |||||||||
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MetaQC Resource Report Resource Website 10+ mentions |
MetaQC (RRID:SCR_006000) | software resource | Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. | standalone software, mac os x, unix/linux, windows, r, FASEB list |
is listed by: OMICtools has parent organization: CRAN |
PMID:22116060 | GNU General Public License, v2 | OMICS_04032 | https://github.com/donkang34/MetaQC | SCR_006000 | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis | 2026-09-12 12:56:34 | 40 | ||||||
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MIALAB - Medical Image Analysis Lab Resource Report Resource Website 10+ mentions |
MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) | MIALAB | data or information resource, laboratory portal, organization portal, portal | MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition. | software, data, data visualization, medical image, image, neuroimaging, fmri, diffusion tensor imaging, electroencephalography, structural imaging, genetic data, brain, image processing, adaptive signal processing, estimation theory, neural network, statistical signal processing, pattern recognition, mri |
has parent organization: Mind Research Network is parent organization of: Group ICA of fMRI Toolbox is parent organization of: Group ICA Of EEG Toolbox is parent organization of: MIALAB - Resting State Data |
Mental disease | nlx_151551 | SCR_006089 | Medical Image Analysis Lab, Medical Image Analysis Laboratory, MIA Laboratory, Medical Image Analysis (MIA) Laboratory | 2026-09-12 12:56:35 | 27 | |||||||
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Scholarly Electronic Publishing Bibliography Resource Report Resource Website |
Scholarly Electronic Publishing Bibliography (RRID:SCR_005949) | SEPB | bibliography, book, data or information resource, narrative resource | Bibliography with over 3,800 selected English-language articles, books, and other printed and electronic sources that are useful in understanding scholarly electronic publishing efforts on the Internet. It covers a wide range of topics, such as digital copyright, digital libraries, digital preservation, digital repositories, e-books, e-journals, license agreements, metadata, and open access. It includes Scholarly Electronic Publishing Resources, a selective directory of related Web sites, and the Scholarly Electronic Publishing Weblog, a frequently updated list of new publications and other resources that may be of interest to bibliography readers. Most sources have been published from January 1, 1990 through October 30, 2011; however, a limited number of earlier key sources are also included. The bibliography includes links to freely available versions of included works. It does not include digital media works (such as MP3 files), editorials, e mail messages, letters to the editor, daily newspaper articles, presentation slides or transcripts, or weblog postings. An archive of prior versions of SEPB is available as a downloadable compressed file (.zip) that includes all versions of the bibliography. The Scholarly Electronic Publishing Bibliography 2010 is available as a paperback (466 pages, $18.95, ISBN-10: 1456453289 and ISBN-13: 9781456453282) and an open access PDF file. | digital copyright, digital library, digital preservation, digital repository, e-book, e-journal, license agreement, metadata, open access, digital publication, digital publication, scholarly, publishing | is listed by: FORCE11 | Creative Commons Attribution-NonCommercial License, v3 United States | nlx_151306 | SCR_005949 | 2026-09-12 12:56:33 | 0 |
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