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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DRUT Resource Report Resource Website |
DRUT (RRID:SCR_004351) | DRUT | software resource | Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data. | c++, reconstruction, frequency estimation, transcript, rna-seq, annotation |
is listed by: OMICtools has parent organization: Georgia State University; Georgia; USA |
NSF IIS-0546457; NSF IIS-0916401; NSF IIS-0916948 |
PMID:23202426 | OMICS_01273 | SCR_004351 | Discovery and Reconstruction of Unannotated Transcripts | 2026-02-07 02:06:22 | 0 | ||||||
|
VS-Lite Resource Report Resource Website 1+ mentions |
VS-Lite (RRID:SCR_002431) | VS-Lite | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation. | model, mathematical model, tree ring, dendrochronology, tree ring width, tree, ring, ring growth model |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
NOAA ; NSF 0724802 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000128 | SCR_002431 | Vaganov-Shashkin-Lite, Vaganov-Shashkin-Lite Model of Tree-Ring Width | 2026-02-07 02:05:44 | 2 | ||||||
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Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-02-07 02:08:08 | 35 | ||||||
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IHM-dictionary Resource Report Resource Website 1+ mentions |
IHM-dictionary (RRID:SCR_016186) | software resource | Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures. | macromolecule, mmcif, pdb, protein, database, databank, spectroscopy, microscopy, crystallography, proteomic | is related to: PDB-Dev | NSF DBI-1519158 | Free, Available for download | SCR_016186 | 2026-02-07 02:09:43 | 3 | |||||||||
|
Microfluidic device to attain high spatial and temporal control of oxygen Resource Report Resource Website |
Microfluidic device to attain high spatial and temporal control of oxygen (RRID:SCR_017131) | instrument resource | Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing. | device, instrument, control, spatial, temporal, variation, oxygen, tension, tissue, microenvironment | NCATS UH3 TR00048; NCI R01 CA170879; NIDDK UC4 DK104202; NSF DGE-1143954 |
PMID:30571786 | SCR_017131 | 2026-02-07 02:10:00 | 0 | ||||||||||
|
BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-02-07 02:06:42 | 11 | ||||||
|
bioKepler Resource Report Resource Website 1+ mentions |
bioKepler (RRID:SCR_005385) | bioKepler | software resource | A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data that is distributed on top of the core Kepler scientific workflow system. | module, bioinformatics, workflow, next-generation sequencing |
is listed by: OMICtools is related to: Kepler is related to: Molecular Dynamics Workflow (BioKepler) |
NSF DBI-1062565 | Acknowledgement requested | OMICS_01139 | SCR_005385 | 2026-02-07 02:07:12 | 2 | |||||||
|
CASHX Resource Report Resource Website 1+ mentions |
CASHX (RRID:SCR_005477) | CASHX | software resource | Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G. |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF MCB-1231726; NIAI AI43288 |
PMID:19307293 | OMICS_00655 | SCR_005477 | Cache ASsisted Hash Search with Xor logic Pipeline, CASHX Pipeline, Cache ASsisted Hash Search with Xor logic | 2026-02-07 02:06:43 | 4 | |||||||
|
Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-02-07 02:06:46 | 7 | ||||||
|
San Diego Supercomputer Center Resource Report Resource Website 1+ mentions |
San Diego Supercomputer Center (RRID:SCR_001856) | SDSC | institution | Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale infrastructure for open scientific research. SDSC currently provides advanced user support and expertise for XSEDE (Extreme Science and Engineering Discovery Environment) the five-year NSF-funded program that succeeded TeraGrid in mid-2011. | engineering, bioinformatics, computing, geoinformatics, hardware, industry, science, software, technology, computational science, supercomputing, cyberinfrastructure |
has parent organization: University of California at San Diego; California; USA is parent organization of: Scaffold builder is parent organization of: OpenTopography is parent organization of: chronopolis is parent organization of: XSEDE - Extreme Science and Engineering Discovery Environment is parent organization of: Family Pairwise Search - Protein Family Classification is parent organization of: Neuroscience Gateway is parent organization of: Magnetics Information Consortium |
NSF | Free, Freely available | nif-0000-10418, Wikidata: Q3947008, grid.419957.7 | https://ror.org/04mg3nk07 | SCR_001856 | 2026-02-07 02:05:45 | 5 | ||||||
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SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-02-07 02:05:23 | 6 | ||||||
|
HapCompass Resource Report Resource Website 1+ mentions |
HapCompass (RRID:SCR_000942) | algorithm | Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings. | algorithm, haplotype, sequence, genome, dna, rna, snp |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
NSF 1048831; NSF 1321000 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00197 | SCR_000942 | 2026-02-07 02:05:24 | 1 | ||||||||
|
Phenex Resource Report Resource Website |
Phenex (RRID:SCR_021748) | software resource | Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data. | phenotype, ontology, taxonomy ontology, taxa, ontology annotations, free text character matrix data, NeXML, evolutionary data | NSF DBI 0641025; NHGRI HG002659; NSF EF0423641 |
DOI:10.1371/journal.pone.0010500 | Free, Available for download, Freely available | https://github.com/phenoscape/Phenex/wiki#download--installation | SCR_021748 | 2026-02-07 02:11:30 | 0 | ||||||||
|
goCognitive Resource Report Resource Website |
goCognitive (RRID:SCR_006154) | goCognitive | assessment test provider, material resource | Free access to materials for students, educators, and researchers in cognitive psychology and cognitive neuroscience. Currently there are about a dozen demonstrations and more than 30 videos that were produced over the last two years. The basic philosophy of goCognitive rests on the assumption that easy and free access to high-quality content will improve the learning experience of students and will enable more students to enjoy the field of cognitive psychology and cognitive neuroscience. There are a few parts of goCognitive that are only available to registered users who have provided their email address, but all of the online demonstrations and videos are accessible to the everyone. Both new demonstrations and new video interviews will continually be added to the site. Manuals for each of the demonstration are being created and available as pdf files for download. Most of the demonstrations are pretty straightforward - but in some cases, especially if you would like to collect data - it might be a good idea to look over the manual. There are different ways in which you can get involved and contribute to the site. Your involvement can range from sending us feedback about the demonstrations and videos, suggestions for new materials, or the simple submission of corrections, to the creation or publication of demonstrations and videos that meet our criteria. Down the road we will make the submission process easier, but for now please contact swerner (at) uidaho dot edu for more information. NSF student grant Undergraduate students can apply through goCognitive for an $1,100 grant to co-produce a new video interview with a leading researcher in the field of cognitive neuroscience. The funding has been provided by the National Science Foundation. | educational tool, education, cognitive neuroscience, interview, demonstration, cognitive psychology, manual, memory, working memory, language processing, neuroscience, long-term memory, linguistics, attention, synesthesia, visual perception, auditory processing, blindspot, change blindness, change detection, declarative memory, dichotic listening, student, educator, researcher, quiz |
is used by: NIF Data Federation is used by: Integrated Videos has parent organization: University of Idaho; Idaho; USA |
Association for Psychological Science ; University of Idaho; Idaho; USA ; NSF ; State of Idaho Board of Education |
Free, A few parts are only available to registered users, The community can contribute to this resource | nlx_151647 | SCR_006154 | GoCognitive - Educational tools for cognitive neuroscience, Go Cognitive | 2026-02-07 02:14:33 | 0 | ||||||
|
Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | authoring tool, software application, software resource | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-02-11 10:56:41 | 147 | |||||
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MorphoBank Resource Report Resource Website 100+ mentions |
MorphoBank (RRID:SCR_003213) | MorphoBank | data or information resource, database | Web application providing online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). It enables researchers to upload images and affiliate data with those images (labels, species names, etc.) and allows researchers to upload morphological data and affiliate it with phylogenetic matrices. MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived. | phenotype, web service, phylogenetics, cladistics, histology, neurology, taxonomy, image, phylogeny, cladistic analysis, morphology, anatomy, evolution, homology, systems biology, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: Stony Brook University; New York; USA |
NSF ; NOAA NA04OAR4700191 |
PMID:34875801 | Free, Freely available | DOI:10.25504/FAIRsharing.1y63n8, DOI:10.17616/R3PC7F, DOI:10.7934, nlx_156938, r3d100010786 | https://doi.org/10.17616/R3PC7F https://doi.org/10.17616/r3pc7f https://doi.org/10.7934/ https://dx.doi.org/10.7934/ https://fairsharing.org/10.25504/FAIRsharing.1y63n8 https://doi.org/10.17616/R3MK88 |
SCR_003213 | 2026-02-11 10:56:37 | 113 | |||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | storage service resource, service resource, data repository | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-02-11 10:59:28 | 35 | |||||||||
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Fungal Genome Initiative Resource Report Resource Website 10+ mentions |
Fungal Genome Initiative (RRID:SCR_003169) | FGI | data or information resource, data set | Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. | sequence, fungi, gene annotation, genome |
is listed by: 3DVC has parent organization: Broad Institute |
NHGRI ; NSF ; NIAID ; USDA |
Free, Freely available | nif-0000-30591 | SCR_003169 | 2026-02-11 10:56:41 | 18 | |||||||
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Sol Genomics Network - Bulk download Resource Report Resource Website |
Sol Genomics Network - Bulk download (RRID:SCR_007161) | data or information resource, data set | Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, dataset, unigene, gene, bac, genomics, clone, array spot, unigene id, bac ends |
is related to: SGN has parent organization: Boyce Thompson Institute for Plant Research |
NSF 0820612; USDA CSREES |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30227 | SCR_007161 | SGN bulk download | 2026-02-11 10:57:29 | 0 | |||||||
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Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets Resource Report Resource Website 1+ mentions |
Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets (RRID:SCR_008921) | Early Indicators of Later Work Levels Disease and Death, EI project | data or information resource, data set | A dataset to advance the study of life-cycle interactions of biomedical and socioeconomic factors in the aging process. The EI project has assembled a variety of large datasets covering the life histories of approximately 39,616 white male volunteers (drawn from a random sample of 331 companies) who served in the Union Army (UA), and of about 6,000 African-American veterans from 51 randomly selected United States Colored Troops companies (USCT). Their military records were linked to pension and medical records that detailed the soldiers������?? health status and socioeconomic and family characteristics. Each soldier was searched for in the US decennial census for the years in which they were most likely to be found alive (1850, 1860, 1880, 1900, 1910). In addition, a sample consisting of 70,000 men examined for service in the Union Army between September 1864 and April 1865 has been assembled and linked only to census records. These records will be useful for life-cycle comparisons of those accepted and rejected for service. Military Data: The military service and wartime medical histories of the UA and USCT men were collected from the Union Army and United States Colored Troops military service records, carded medical records, and other wartime documents. Pension Data: Wherever possible, the UA and USCT samples have been linked to pension records, including surgeon''''s certificates. About 70% of men in the Union Army sample have a pension. These records provide the bulk of the socioeconomic and demographic information on these men from the late 1800s through the early 1900s, including family structure and employment information. In addition, the surgeon''''s certificates provide rich medical histories, with an average of 5 examinations per linked recruit for the UA, and about 2.5 exams per USCT recruit. Census Data: Both early and late-age familial and socioeconomic information is collected from the manuscript schedules of the federal censuses of 1850, 1860, 1870 (incomplete), 1880, 1900, and 1910. Data Availability: All of the datasets (Military Union Army; linked Census; Surgeon''''s Certificates; Examination Records, and supporting ecological and environmental variables) are publicly available from ICPSR. In addition, copies on CD-ROM may be obtained from the CPE, which also maintains an interactive Internet Data Archive and Documentation Library, which can be accessed on the Project Website. * Dates of Study: 1850-1910 * Study Features: Longitudinal, Minority Oversamples * Sample Size: ** Union Army: 35,747 ** Colored Troops: 6,187 ** Examination Sample: 70,800 ICPSR Link: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06836 | late adult human, male, caucasian, african-american, veteran, military, medical, socioeconomic, civil war, american civil war, cause of death, census data, demographic, disease, health status, labor force, medical record, midlife, military pension, pension, military recruitment, military service, mortality rate, nineteenth century, nutrition, socioeconomic status, twentieth century, union army, census |
is related to: National Archive of Computerized Data on Aging (NACDA) has parent organization: University of Chicago; Illinois; USA |
Aging | NIA PO1 AG10120; NSF SBR 9114981 |
Publicly available from ICPSR; copies on CD-ROM may be obtained from the CPE, Which also maintains an interactive Internet Data Archive and Documentation Library. | nlx_151822 | http://www.cpe.uchicago.edu/ | SCR_008921 | Public Health and Ecological Datasets, Aging of Veterans of the Union Army, Early Indicators of Later Work Levels Disease and Death ������?? Union Army Samples | 2026-02-11 10:57:53 | 1 |
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