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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Brain Science Podcast Resource Report Resource Website |
Brain Science Podcast (RRID:SCR_004491) | BSP | narrative resource, podcast, data or information resource | Podcast, hosted by Dr. Ginger Campbell, featuring the latest books about neuroscience as well as interviews with leading scientists from around the world. In this podcast, she shares recent discoveries from the world of neuroscience in a way that people of all backgrounds can enjoy. Dr. Campbell is an experienced emergency physician with a long-standing interest in mind-body medicine, the brain, and consciousness. She believes that understanding how the brain works gives us insight into what makes us human. She is also committed to showing how the scientific method has unraveled many long-standing mysteries. Brain Science Transcripts are also available. | neuroscience, brain, interview, consciousness, mind |
is used by: NIF Data Federation is related to: Integrated Podcasts |
nlx_47745 | SCR_004491 | 2026-08-01 12:02:37 | 0 | |||||||||
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Basic OligoNucleotide Design Resource Report Resource Website 10+ mentions |
Basic OligoNucleotide Design (RRID:SCR_004492) | BOND | software resource | Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. | dna, oligonucleotide, design, oligonucleotide design |
is listed by: OMICtools has parent organization: Western University; Ontario; Canada |
PMID:23444904 | OMICS_00827 | SCR_004492 | BOND: Basic OligoNucleotide Design | 2026-08-01 12:02:42 | 17 | |||||||
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UniProtKB Subcellular Locations Resource Report Resource Website 10+ mentions |
UniProtKB Subcellular Locations (RRID:SCR_004373) | SP SL | ontology, controlled vocabulary, data or information resource, database | The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. You may search in subcellular locations or list them all along with their definitions (490). By default, searching the subcellular locations will look for matches in both name and definition. | has parent organization: UniProtKB | nlx_38886 | SCR_004373 | UniProt Subcellular Locations | 2026-08-01 12:02:36 | 16 | |||||||||
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HelioScan Resource Report Resource Website 10+ mentions |
HelioScan (RRID:SCR_004494) | HelioScan | software resource | HelioScan is a versatile control software for microscopes written in the intuitive graphical programming language LabVIEW. It solves a number of problems observed with custom-built image acquisition systems by providing the following features: * Extendability: both hardware components and software functionality are encapsulated in exchangeable, software components. Additional components can be implemented easily and plugged in at run-time. Components can be independently developed, allowing multiple developers to work in parallel. * Flexibility: Components are independently configurable; each component can have an unlimited number of configurations. * Understandability: The LabVIEW code is well-structured, commented and documented. * High speed: The software supports FPGA-based hardware that enables intelligent and extremely fast signal acquisition and generation. FPGA logic can be easily programmed using LabVIEW. * Tailored to in vivo brain imaging: The software is especially suited for 2-photon Calcium imaging, but can in principle be used for any kind of microscopy. The out-of-the-box software supports different imaging modalities (camera, galvanometric scan mirrors, acusto-optic deflectors) and imaging modes (camera video acquisition, intrinsic optical imaging, two-photon frame scan and tilted frame scan, 2D line scan, 3D spiral scan) and can easily be extended to other imaging modalities (e.g., resonance scanners), imaging modes (e.g., 2D and 3D arbitrary line scans) and associated hardware (e.g., stimulation devices). * Open file-format with extensible meta-data schema: HelioScan saves data in the OME-TIFF file format, which contains image data as multipage TIFF and meta-data as human-readable XML in the TIFF description tag according to the OME schema. | microscopy, two photon, calcium imaging, light microscopy, multiphoton imaging protocol, calcium(2+), imaging, brain, brain imaging | has parent organization: ETH Zurich; Zurich; Switzerland | nlx_143787 | SCR_004494 | Helio Scan | 2026-08-01 12:02:37 | 11 | ||||||||
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Catalog of Fishes Resource Report Resource Website |
Catalog of Fishes (RRID:SCR_004408) | CASGEN, CASSPC, CASREF, | data or information resource, narrative resource, database, book, bibliography | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes. | genus, species, reference, publication |
is related to: Teleost Taxonomy Ontology is related to: Phenoscape Knowledgebase has parent organization: California Academy of Sciences |
NSF ; Alfred P. Sloan Foundation |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41737 | SCR_004408 | Catalog of Fishes database | 2026-08-01 12:02:37 | 0 | ||||||
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National Drug Abuse Treatment Clinical Trials Network Resource Report Resource Website |
National Drug Abuse Treatment Clinical Trials Network (RRID:SCR_004407) | CTN | consortium, clinical trial, data or information resource, portal, organization portal | A collaboration in which the National Institute on Drug Abuse, treatment researchers, and community-based service providers cooperatively develop, validate, refine, and deliver new treatment options to patients in Community Treatment Programs (CTPs). The partnership between CTPs and academic research leaders aims to achieve the following objectives: * Conducting studies of behavioral, pharmacological, and integrated behavioral and pharmacological treatment interventions of therapeutic effect in rigorous, multisite clinical trials to determine effectiveness across a broad range of community-based treatment settings and diversified patient populations; and * Ensuring the transfer of research results to physicians, clinicians, providers, and patients. The CTN, with its core of CTPs engaging diverse populations, is also designed to provide a platform for other studies, which would be funded under separate research grants. Three important ways to use the CTN are: to conduct ancillary studies in connection with CTN protocols; to utilize CTN Node facilities as a platform for investigations; and for Nodes to serve as home bases for NIH Training Centers and individual researchers who have NIH fellowships or career development awards. | drug of abuse, substance abuse, addiction, behavioral, clinical, clinical trial, pharmacological, therapy, treatment |
has parent organization: National Institute on Drug Abuse is parent organization of: NIDA Data Share |
nif-0000-00227 | SCR_004407 | NIDA CTN | 2026-08-01 12:02:40 | 0 | ||||||||
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HUPO Antibody Initiative Resource Report Resource Website 1+ mentions |
HUPO Antibody Initiative (RRID:SCR_004568) | HAI | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.The mission of the Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The initiative consists of two separate activities; (1) the generation of a catalogue of validated antibodies from many different sources and (2) a protein atlas for the expression and localization of human proteins in normal and disease tissue. The two separate activities have as their primary deliverables to generate databases with free public accessibility. The Antibody Resource database (www.antibodypedia.org) is aimed to produce a comprehensive catalogue of validated antibodies towards human proteins. This initiative depends on input from a large number of academic groups and commercial companies. The Protein Atlas initiative (www.proteinatlas.org) is aimed to provide comprehensive and annotated database of high-resolution images showing tissue profiles in normal and cancer tissues. Both databases will be open to the public without restriction (no passwords). | antibody, human |
has parent organization: HUPO - Human Proteome Organisation is parent organization of: The Human Protein Atlas |
Knut and Alice Wallenberg Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_56399 | http://www.hupo.org/research/hai/ | SCR_004568 | HUPO Human Antibody Initiative, HUPO HAI, Human Antibody Initiative | 2026-08-01 12:02:42 | 1 | |||||
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Brighter Ideas Inc. Resource Report Resource Website |
Brighter Ideas Inc. (RRID:SCR_004689) | commercial organization, antibody supplier, reagent supplier, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. An Antibody supplier | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152322 | SCR_004689 | Bii, Brighter Ideas Inc., Brighter Ideas Inc | 2026-08-01 12:02:43 | 0 | ||||||||||
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Oscar3 Resource Report Resource Website 1+ mentions |
Oscar3 (RRID:SCR_004561) | Oscar | software resource | OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/ | annotation, chemistry |
is related to: U-Compare has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21999457 | nlx_55584 | SCR_004561 | OSCAR, Open Source Chemistry Analysis Routines | 2026-08-01 12:02:42 | 3 | |||||||
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Mouse Brain Architecture Project Resource Report Resource Website 1+ mentions |
Mouse Brain Architecture Project (RRID:SCR_004683) | atlas, data or information resource, d spatial image, reference atlas | An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset. | atlas, brain, brain architecture, connectivity, mouse brain architecture, neuroanatomy |
is related to: Brain Architecture Project has parent organization: Brain Architecture Project |
NIH Office of the Director ; NIMH RC1MH088659; NIMH R01MH087988 |
Fully accessible to the neuroscience community as well as interested members of the general public, Acknowledgement requested | nlx_146201 | http://www.brainarchitecture.org | http://www.brainarchitecture.org/mouse/about | SCR_004683 | MBA Project, Mouse Brain Architecture | 2026-08-01 12:02:39 | 5 | |||||
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Handbook of Genetic Counseling Resource Report Resource Website |
Handbook of Genetic Counseling (RRID:SCR_004564) | Handbook of Genetic Counseling | book, narrative resource, data or information resource, wiki | The Handbook of Genetic Counseling is a wikibook designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged. Wikibooks contains books on many medical topics; however, no warranty whatsoever is made that any of the books are accurate. | gene, counseling, genetic, syndrome, disease | has parent organization: Wikibooks | nlx_79147 | SCR_004564 | 2026-08-01 12:02:41 | 0 | |||||||||
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SOrt-ITEMS Resource Report Resource Website 1+ mentions |
SOrt-ITEMS (RRID:SCR_004716) | SOrt-ITEMS | software resource | Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, taxonomy, sequence, orthology, binning | is listed by: OMICtools | PMID:19439565 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01465 | SCR_004716 | Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences, SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences | 2026-08-01 12:02:44 | 6 | ||||||
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PGN Resource Report Resource Website |
PGN (RRID:SCR_004559) | PGN | data analysis service, data or information resource, data repository, storage service resource, database, service resource, data set, production service resource, analysis service resource | Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future. | expressed sequence tag, genomics, functional annotation, blast, sequencing, chromatogram | has parent organization: Cornell University; New York; USA | NSF DBI-9872617; NSF DBI-0115684 |
nlx_55223 | SCR_004559 | PGN - Plant Genome Network, Plant Genome Network | 2026-08-01 12:02:37 | 0 | |||||||
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Orthopaedic Surgery Resource Report Resource Website 1+ mentions |
Orthopaedic Surgery (RRID:SCR_004715) | book, narrative resource, data or information resource, wiki | Orthopaedic Surgery is a collaborative wikibook of orthopedic surgery. *Preface *Chapter 1: Basic Sciences *Chapter 2: Upper Limb *Chapter 3: Foot and Ankle *Chapter 4: Spine *Chapter 5: Hand and Microsurgery *Chapter 6: Pediatric Orthopedics *Chapter 7: Adult Reconstruction *Chapter 8: Sports Medicine *Chapter 9: Musculoskeletal Tumors *Chapter 10: Injury *Chapter 11: Surgical Procedures *Chapter 12: Rehabilitation *Chapter 13: Practice | has parent organization: Wikibooks | nlx_71236 | SCR_004715 | Orthopaedic Surgery (wikibook), Orthopedic Surgery | 2026-08-01 12:02:39 | 1 | ||||||||||
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National University of Ireland; Galway; Ireland Resource Report Resource Website 1+ mentions |
National University of Ireland; Galway; Ireland (RRID:SCR_004677) | NUI Galway | university | Located in the city of Galway in Ireland. |
is affiliated with: Big Data Public Private Forum is related to: Pharma-Planta Consortium is related to: Biomedical Diagnostics Institute is parent organization of: Digital Enterprise Research Institute |
grid.6142.1, Wikidata:Q644478, Crossref funder ID:501100001634, ISNI:0000 0004 0488 0789, nlx_149500 | https://ror.org/03bea9k73 | SCR_004677 | National University of Ireland, National University of Ireland Galway | 2026-08-01 12:02:39 | 1 | ||||||||
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UnifiedGenotyper Resource Report Resource Website 500+ mentions |
UnifiedGenotyper (RRID:SCR_004710) | UnifiedGenotyper | software resource | A multiple-sample, technology-aware SNP and indel caller. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00080 | SCR_004710 | 2026-08-01 12:02:44 | 561 | ||||||||||
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CBLAST Resource Report Resource Website 1+ mentions |
CBLAST (RRID:SCR_004711) | analysis service resource, service resource, production service resource, d spatial image | The NCBI Related Structures tool allows you to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein. CBLAST is a tool that compares a query protein sequence against all protein sequences from resolved 3D structures by using protein BLAST against the PDB data set. The purpose is to find representative 3D structures for the query and/or its homologs, as available. Each record in the Entrez Protein database has been CBLAST''ed and the search results are available as Related Structures in the Links menu of Entrez Protein records. You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records. The search results can be viewed in Cn3D (hence the name CBLAST), which displays an alignment of the query protein to the related structure''s sequence and allows you to interactively examine the sequence-structure relationship. | gold standard |
is related to: NCBI Structure has parent organization: NCBI |
PMID:17135201 | nlx_70506 | SCR_004711 | NCBI Related Structures, NCBI Related Structure Search | 2026-08-01 12:02:39 | 2 | ||||||||
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Open Medicine Live Wiki Resource Report Resource Website |
Open Medicine Live Wiki (RRID:SCR_004550) | Open Medicine Live | narrative resource, data or information resource, wiki | This project explores the use of a wiki as an online collaborative tool for improving and updating peer-reviewed systematic reviews. Posted on this wiki is a copy of the article: Second-line therapy in patients with type 2 diabetes inadequately controlled with metformin monotherapy: A systematic review and mixed treatment comparisons meta-analysis. Readers are invited to edit the article by adding to, deleting or modifying its contents. | metformin, treatment | Type 2 diabetes mellitus | Content:, Creative Commons Attribution-ShareAlike License, v3 Unported | nlx_54196 | SCR_004550 | Open Medicine: where articles Live | 2026-08-01 12:02:37 | 0 | |||||||
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Systems Biology Graphical Notation Resource Report Resource Website 1+ mentions |
Systems Biology Graphical Notation (RRID:SCR_004671) | SBGN | data or information resource, international standard specification, portal, narrative resource, meeting resource, standard specification, topical portal, software resource, training resource | The Systems Biology Graphical Notation (SBGN) project aims to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word. Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. A list of software packages known to provide (or have started to develop) support for SBGN notations is available. | New Energy and Industrial Technology Development Organization ; Okinawa Institute of Science and Technology ; BBSRC ; National Institute of Advanced Industrial Science and Technology of Japan ; European Media Laboratory EML Research GmbH ; California Institute of Technology; California; USA ; NIGMS 1R01GM081070-01 |
PMID:19668183 | nlx_66628 | SCR_004671 | 2026-08-01 12:02:43 | 1 | |||||||||
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Capralogics Resource Report Resource Website 1+ mentions |
Capralogics (RRID:SCR_004673) | commercial organization | An Antibody supplier | nlx_152324 | SCR_004673 | Capralogics Inc. | 2026-08-01 12:02:43 | 1 |
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