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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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COBALT: Constraint-based Multiple Alignment Tool Resource Report Resource Website 10+ mentions |
COBALT: Constraint-based Multiple Alignment Tool (RRID:SCR_004152) | computation service resource, software resource | COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. Pairwise constraints are then incorporated into a progressive multiple alignment. A Linux executable for COBALT, and CDD and PROSITE data used is available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt/ COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems. | gold standard | has parent organization: NCBI | PMID:17332019 | nlx_17358 | SCR_004152 | NCBI COBALT, NCBI Constraint-based Multiple Alignment Tool, Constraint-based Multiple Alignment Tool | 2026-08-12 10:48:55 | 10 | ||||||||
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NIH Toolbox Flanker Inhibitory Control and Attention Test Resource Report Resource Website 1+ mentions |
NIH Toolbox Flanker Inhibitory Control and Attention Test (RRID:SCR_003617) | Flanker task | material resource, assessment test provider | Assessment test that measures both a participant''s attention and inhibitory control. The test requires the participant to focus on a given stimulus while inhibiting attention to stimuli (fish for ages 3-7 or arrows for ages 8-85) flanking it. Sometimes the middle stimulus is pointing in the same direction as the flankers (congruent) and sometimes in the opposite direction (incongruent). Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 3 minutes to administer. This test is recommended for ages 3-85. | cognition, attention, executive function, inhibitory control | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157770 | SCR_003617 | Flanker Inhibitory Control and Attention Test | 2026-08-12 10:48:50 | 1 | ||||||||
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NIH Toolbox Dimensional Change Card Sort Test Resource Report Resource Website 1+ mentions |
NIH Toolbox Dimensional Change Card Sort Test (RRID:SCR_003616) | DCCS | material resource, assessment test provider | Assessment test that measures the cognitive flexibility of patients. Two target pictures are presented that vary along two dimensions (e.g., shape and color). Participants are asked to match a series of bivalent test pictures (e.g., yellow balls and blue trucks) to the target pictures, first according to one dimension (e.g., color) and then, after a number of trials, according to the other dimension (e.g., shape). Switch trials are also employed, in which the participant must change the dimension being matched. For example, after 4 straight trials matching on shape, the participant may be asked to match on color on the next trial and then go back to shape, thus requiring the cognitive flexibility to quickly choose the correct stimulus. Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 4 minutes to administer. This test is recommended for ages 3-85. | cognitive flexibility, cognition, executive function | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157769 | SCR_003616 | 2026-08-12 10:48:50 | 2 | |||||||||
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Alien hunter Resource Report Resource Website 1+ mentions |
Alien hunter (RRID:SCR_004575) | software resource, software application | Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer. |
is listed by: SoftCite has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:16837528 | nlx_56835 | SCR_004575 | Alien_hunter: Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA | 2026-08-12 10:49:00 | 3 | |||||||||
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Platypus Resource Report Resource Website 100+ mentions |
Platypus (RRID:SCR_005389) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data. | Haplotype based variant caller, next generation sequence data, gene, genomic, high throughput sequencing data, |
is listed by: OMICtools is related to: SAMTOOLS has parent organization: Wellcome Trust Centre for Human Genetics |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009046, nlx_154021, OMICS_00068 | SCR_005389 | Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data, PLAYPUS | 2026-08-12 10:49:09 | 200 | ||||||||
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Social Phobia Inventory Resource Report Resource Website 1+ mentions |
Social Phobia Inventory (RRID:SCR_003673) | SPIN | material resource, assessment test provider | A 17-item self-administered assessment questionnaire developed by the Psychiatry and Behavioral Sciences Department at Duke University effective in screening for and measuring the severity of social anxiety disorder. Each question is answered with one of 5 responses ranging from Not at All to Extremely. Each response is assigned a score and then totaled at the end. Scoring: * 0-20 Little or No Anxiety * 21-30 Mild Anxiety * 31-40 Moderate Anxiety * 41-50 Severe Anxiety * 51-68 Very Severe Anxiety | questionnaire | Social anxiety disorder | Free | nlx_157827 | SCR_003673 | 2026-08-12 10:48:51 | 1 | ||||||||
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Substructure Index-based Approximate Graph Alignment Resource Report Resource Website 10+ mentions |
Substructure Index-based Approximate Graph Alignment (RRID:SCR_003434) | SAGA | software resource, software application | SAGA (Substructure Index-based Approximate Graph Alignment) is a tool for querying a biological graph database to retrieve matches between subgraphs of molecular interactions and biological networks. SAGA implements an efficient approximate subgraph matching algorithm that can be used for a variety of biological graph matching problems such as the pathway matching SAGA uses to compare pathways in KEGG and Reactome. You can also use SAGA to find matches in literature databases that have been parsed into semantic graphs. In this use of SAGA, portions of PubMed have been parsed into graphs that have nodes representing gene names. A link is drawn between two genes if they are discussed in the same sentence (indicating there is potential association between the two genes). SAGA lets you match graphs between different databases even though the content is distinct and the databases organize pathways in different ways. This cross-database matching is achieved by SAGA's flexible approximate subgraph matching model that computes graph similarity, and allows for node gaps, node mismatches, and graph structural differences. Comparing pathways from different databases can be a useful precursor to pathway data integration. SAGA is very efficient for querying relatively small graphs, but becomes prohibitory expensive for querying large graphs. Large graph data sets are common in many emerging database applications, and most notably in large-scale scientific applications. To fully exploit the wealth of information encoded in graphs, effective and efficient graph matching tools are critical. Due to the noisy and incomplete nature of real graph datasets, approximate, rather than exact, graph matching is required. Furthermore, many modern applications need to query large graphs, each of which has hundreds to thousands of nodes and edges. TALE is an approximate subgraph matching tool for matching graph queries with a large number of nodes and edges. TALE employs a novel indexing technique that achieves a high pruning power and scales linearly with the database size. | gene, algorithm, alignment, biological, graph, interaction, literature, molecular, pathway, query, reactome, structural, subgraph, substructure, tool, graph similarity |
is listed by: Biositemaps has parent organization: National Center for Integrative Biomedical Informatics has parent organization: University of Michigan; Ann Arbor; USA |
Microsoft ; NIDA 1-U54-DA021519-01A1 |
PMID:17110368 | Access free via the web; Binaries are also freely available. If you use SAGA for any work that leads to a publication you must cite paper. | nif-0000-33157 | SCR_003434 | SAGA (Substructure Index-based Approximate Graph Alignment), SAGA - Substructure Index-based Approximate Graph Alignment, SAGA: A Fast and Flexible Graph Matching Tool | 2026-08-12 10:48:48 | 24 | |||||
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Kickstarter Resource Report Resource Website 10+ mentions |
Kickstarter (RRID:SCR_004246) | Kickstarter | funding resource, service resource | Kickstarter is the world''s largest funding platform for creative projects. Every week, tens of thousands of amazing people pledge millions of dollars to projects from the worlds of music, film, art, technology, design, food, publishing and other creative fields. A new form of commerce and patronage. This is not about investment or lending. Project creators keep 100% ownership and control over their work. Instead, they offer products and experiences that are unique to each project. All or nothing funding. On Kickstarter, a project must reach its funding goal before time runs out or no money changes hands. Why? It protects everyone involved. Creators aren''t expected to develop their project without necessary funds, and it allows anyone to test concepts without risk. Each and every project is the independent creation of someone like you. Projects are big and small, serious and whimsical, traditional and experimental. They''re inspiring, entertaining and unbelievably diverse. We hope you agree... Welcome to Kickstarter! | nlx_143647 | SCR_004246 | 2026-08-12 10:48:56 | 19 | |||||||||||
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Hamilton Anxiety Rating Scale Resource Report Resource Website 1+ mentions |
Hamilton Anxiety Rating Scale (RRID:SCR_003664) | HAM-A | material resource, assessment test provider | Assessment scale to assess the severity of symptoms of anxiety in adults, adolescents and children. The scale consists of 14 items, each defined by a series of symptoms, and measures both psychic anxiety (mental agitation and psychological distress) and somatic anxiety (physical complaints related to anxiety). Although the HAM-A remains widely used as an outcome measure in clinical trials, it has been criticized for its sometimes poor ability to discriminate between anxiolytic and antidepressant effects, and somatic anxiety versus somatic side effects. The HAM-A does not provide any standardized probe questions. Despite this, the reported levels of inter-rater reliability for the scale appear to be acceptable. The scale has been translated into: Cantonese for China, French and Spanish. An IVR version of the scale is available from Healthcare Technology Systems. | adult human, adolescent, child, clinician | has parent organization: National Institute of Neurological Disorders and Stroke | Anxiety | Public domain | nlx_157820 | http://psychology-tools.com/hamilton-anxiety-rating-scale/ | SCR_003664 | Hamilton Anxiety Rating Scale (HAM-A) | 2026-08-12 10:48:50 | 2 | |||||
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MILD Resource Report Resource Website 100+ mentions |
MILD (RRID:SCR_003335) | MILD | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software). | gene, genetic, genomic, unix, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154480 | SCR_003335 | MultIallelic Linkage Disequilibrium: a program for adjusted linkage disequilibrium (LD) calculations | 2026-08-12 10:48:47 | 106 | |||||||
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PAWE-3D Resource Report Resource Website 1+ mentions |
PAWE-3D (RRID:SCR_003326) | PAWE-3D | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | PMID:16123114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154481 | SCR_003326 | Power for Association With Error in 3D | 2026-08-12 10:48:46 | 2 | ||||||
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Structured Clinical Interview for DSM-IV Resource Report Resource Website 1+ mentions |
Structured Clinical Interview for DSM-IV (RRID:SCR_003682) | SCID, SCID-I, SCID-II | material resource, assessment test provider | A diagnostic exam used to determine DSM-IV Axis I disorders (SCID-I) (major mental disorders) and Axis II disorders (SCID-II) (personality disorders). An Axis I SCID assessment with a psychiatric patient usually takes between 1 and 2 hours, depending on the complexity of the subject's psychiatric history and their ability to clearly describe episodes of current and past symptoms. A SCID with a non-psychiatric patient takes 1/2 hour to 1-1/2 hours. A SCID-II personality assessment takes about 1/2 to 1 hour. The instrument was designed to be administered by a clinician or trained mental health professional. (Adapter from Wikipedia) | clinical, mental health, semi-structured interview, interview | Mental disease, Personality disorder | Acknowledgement requested, Commercial license | nlx_157838 | SCR_003682 | 2026-08-12 10:48:51 | 8 | ||||||||
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Mini-Mental State Examination Resource Report Resource Website 100+ mentions |
Mini-Mental State Examination (RRID:SCR_003681) | MMSE | material resource, assessment test provider | A 30 question assessment test to screen patients for cognitive impairment that is commonly used in medicine to screen for dementia. It is also used to estimate the severity of cognitive impairment and to follow the course of cognitive changes in an individual over time, thus making it an effective way to document an individual's response to treatment. It takes about 10 minutes and examines functions including arithmetic, memory and orientation. | questionnaire, late adult human, memory, cognition, arithmetic, orientation | is related to: Standardized Mini-Mental State Examination | Cognitive impairment, Dementia | Copyrighted | nlx_157834 | SCR_003681 | Folstein Test, Mini-Mental State Examination (MMSE) | 2026-08-12 10:48:51 | 414 | ||||||
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(at)Note Resource Report Resource Website 1+ mentions |
(at)Note (RRID:SCR_005342) | (at)Note | text-mining software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels. | java, java swt, text, mining |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Minho; Braga; Portugal |
PMID:19393341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01167 | SCR_005342 | (at)Note2 - A workbench for Biomedical Text Mining | 2026-08-12 10:49:09 | 2 | ||||||
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Childhood Autism Spectrum Test Resource Report Resource Website 10+ mentions |
Childhood Autism Spectrum Test (RRID:SCR_003322) | CAST | material resource, assessment test provider | Assessment test developed by the Autism Research Centre at the University of Cambridge, for assessing the severity of autism spectrum symptoms in children. This assessment is usually used with children aged from 4-11 years of age. | child, young human | Pervasive Development Disorder, Autism | Free, Freely available | nlx_157819 | http://www.moodychild.com/uploads/3/0/8/9/3089108/cast_autism.pdf | SCR_003322 | Childhood Autism Spectrum Test (CAST), Childhood Asperger''s Syndrome Test | 2026-08-12 10:48:46 | 22 | ||||||
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Clinical Dementia Rating Resource Report Resource Website 100+ mentions |
Clinical Dementia Rating (RRID:SCR_003678) | CDR | material resource, assessment test provider | A numeric scale used to quantify the severity of symptoms of dementia (i.e. its stage). Using a structured-interview protocol, a qualified health professional assesses a patient's cognitive and functional performance in six areas: memory, orientation, judgment and problem solving, community affairs, home and hobbies, and personal care. Scores in each of these are combined to obtain a composite score ranging from 0 through 3. (Adapted from Wikipedia) | memory, orientation, judgment, problem solving, community, hobby, personal care, late adult human | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | Dementia, Alzheimer's disease | Free | nlx_157831 | SCR_003678 | Global CDR Assignment Based On Box Scores, Global Clinical Dementia Rating (CDR) Based on CDR Box Scores | 2026-08-12 10:48:50 | 237 | ||||||
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BETA Resource Report Resource Website 100+ mentions |
BETA (RRID:SCR_007556) | BETA | software resource, software application | Software application for non-parametric linkage analysis using allele sharing in sib pairs (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, sun | is listed by: Genetic Analysis Software | nlx_154241 | SCR_007556 | 2026-08-12 10:49:48 | 138 | |||||||||
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MAPCREATOR Resource Report Resource Website 1+ mentions |
MAPCREATOR (RRID:SCR_008001) | MAPCREATOR | software resource, software application | Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | nlx_154455 | SCR_008001 | 2026-08-12 10:49:44 | 4 | |||||||||
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PhenoTips Resource Report Resource Website 10+ mentions |
PhenoTips (RRID:SCR_006340) | PhenoTips | software resource, software application | A software tool providing a Web interface and a database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. The main goals of this software are * To allow for collecting patient data in standard formats, enabling effortless data exchange and automated search in annotated gene and disease databases, and * To provide advanced functionalities and a friendly user interface that help reduce the clinician''''s workload, permitting seamless use of this application within the clinician''''s routine. PhenoTips uses the Human Phenotype Ontology (HPO) to express clinical phenotypes, and provides a friendly interface with error-tolerant, predictive search of phenotypic descriptions. PhenoTips closely mirrors clinician workflows: observations can be recorded directly during the patient encounter, and the interface is compatible with any device that runs a modern Web browser. The clinician can record demographic information, family history, medical history, various standard measurements, phenotypic abnormalities detected in the patient, pertinent indications that were not observed and that can be helpful for differential diagnosis, relevant images depicting manifestations of the patient''''s disorders, and additional notes for each of these categories. The software automatically plots growth curves, selects phenotypes reflecting abnormal measurements, instantly finds OMIM disorders matching the phenotypic description and suggests other symptoms to investigate in order to reach a more accurate diagnosis. | clinical symptom, physical finding, clinical, phenotype, demographic information, family history, medical history, standard measurement, indication, image, note, growth curve |
is related to: Human Phenotype Ontology is related to: OMIM has parent organization: University of Toronto; Ontario; Canada |
Genetic disorder | Free | nlx_152049 | SCR_006340 | PhenoTips: phenotyping made easy | 2026-08-12 10:49:24 | 24 | ||||||
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Graphical Overview of Linkage Disequilibrium Resource Report Resource Website 1000+ mentions |
Graphical Overview of Linkage Disequilibrium (RRID:SCR_007151) | GOLD | software resource, software application | Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:10842743 | nlx_154363 | SCR_007151 | 2026-08-12 10:49:41 | 2212 |
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