132,851 research outputs found
TAIR functional annotation data
No full textQuarterly release of curated gene function data for Arabidopsis thaliana from The Arabidopsis Information Resource (www.arabidopsis.org)
The contents of the compressed archive include the following files which are described in detail in the included README file.
1.ATH_GO_GOSLIM.txt.gz
This document is a tab-delimited file containing GO annotations for Arabidopsis genes annotated by TAIR and TIGR with terms from the Gene Ontology Consortium controlled vocabularies (see www.geneontology.org). This file includes an updated set of literature based annotations and >40,000 electronic annotations based upon matches to INTERPRO domains supplied by Nicola Mulder from SWISS PROT/INTERPRO.
Please cite this paper when using TAIR's GO annotations in your research: Berardini, TZ, Mundodi, S, Reiser, L, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11.
2.gene_aliases_yyyymmdd.txt(.gz)
This file lists alternative names for each gene.
3.Locus_Germplasm_Phenotype_yyyymmdd.txt.gz
This file contains links between loci, germplasms, and phenotypes.
4.Locus_Published_yyyymmdd.txt.gz
This file contains links between loci and publications.
5.po_temporal_gene_arabidopsis_tair.assoc.gz
po_anatomy_gene_arabidopsis_tair.assoc.gz
These two files are tab-delimited files. Each contains the
set of literature-based annotations of Arabidopsis genes and loci annotated at TAIR to the terms from the Plant Ontology developed by the Plant Ontology Consortium (POC, www.plantontology.org).
6.TAIR10 or ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz)
This file contains functional descriptions for gene models included in either the TAIR 10 or as of 20170630 the Araport11 genome release. TAIR10/Araport11 refers to the version of the genome annotation.
</p
TAIR functional annotation data
No full textQuarterly release of curated gene function data for Arabidopsis thaliana from The Arabidopsis Information Resource (www.arabidopsis.org)
The contents of the compressed archive include the following files which are described in detail in the included README file.
1.ATH_GO_GOSLIM.txt.gz
This document is a tab-delimited file containing GO annotations for Arabidopsis genes annotated by TAIR and TIGR with terms from the Gene Ontology Consortium controlled vocabularies (see www.geneontology.org). This file includes an updated set of literature based annotations and >40,000 electronic annotations based upon matches to INTERPRO domains supplied by Nicola Mulder from SWISS PROT/INTERPRO.
Please cite this paper when using TAIR's GO annotations in your research: Berardini, TZ, Mundodi, S, Reiser, L, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11.
2.gene_aliases_yyyymmdd.txt(.gz)
This file lists alternative names for each gene.
3.Locus_Germplasm_Phenotype_yyyymmdd.txt.gz
This file contains links between loci, germplasms, and phenotypes.
4.Locus_Published_yyyymmdd.txt.gz
This file contains links between loci and publications.
5.po_temporal_gene_arabidopsis_tair.assoc.gz
po_anatomy_gene_arabidopsis_tair.assoc.gz
These two files are tab-delimited files. Each contains the
set of literature-based annotations of Arabidopsis genes and loci annotated at TAIR to the terms from the Plant Ontology developed by the Plant Ontology Consortium (POC, www.plantontology.org).
6.TAIR10 or ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz)
This file contains functional descriptions for gene models included in either the TAIR 10 or as of 20170630 the Araport11 genome release. TAIR10/Araport11 refers to the version of the genome annotation.
</p
Free energy minimization approach to penetration of resonant magnetic perturbations in tokamaks
No full textBy applying the principle of minimum free energy an analytical model for the plasma response to externally applied resonant magnetic perturbations (RMPs) is proposed. The results are compared with ATTEMPT code calculations [D. Reiser , Phys. Plasmas 16, 0042317 (2009)] and reproduce qualitatively and quantitatively the numerical results on the collisionality dependence of RMP penetration characteristics. Strong increase in the radial electric field with reduced screening at RMPs above a certain threshold is also reproduced by the model
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
TAIR functional annotation data
No full text<p>Quarterly release of curated gene function data for Arabidopsis thaliana from The Arabidopsis Information Resource (www.arabidopsis.org)</p>
<p>The contents of the compressed archive include the following files which are described in detail in the included README file.</p>
<p><br>
1.ATH_GO_GOSLIM.txt.gz<br>
This document is a tab-delimited file containing GO annotations for Arabidopsis genes annotated by TAIR and TIGR with terms from the Gene Ontology Consortium controlled vocabularies (see www.geneontology.org). This file includes an updated set of literature based annotations and >40,000 electronic annotations based upon matches to INTERPRO domains supplied by Nicola Mulder from SWISS PROT/INTERPRO. </p>
<p>Please cite this paper when using TAIR's GO annotations in your research: Berardini, TZ, Mundodi, S, Reiser, L, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11. </p>
<p><br>
2.gene_aliases_yyyymmdd.txt(.gz)<br>
This file lists alternative names for each gene.</p>
<p><br>
3.Locus_Germplasm_Phenotype_yyyymmdd.txt.gz<br>
This file contains links between loci, germplasms, and phenotypes. <br>
<br>
4.Locus_Published_yyyymmdd.txt.gz<br>
This file contains links between loci and publications. <br>
<br>
5.po_temporal_gene_arabidopsis_tair.assoc.gz<br>
po_anatomy_gene_arabidopsis_tair.assoc.gz<br>
These two files are tab-delimited files. Each contains the <br>
set of literature-based annotations of Arabidopsis genes and loci annotated at TAIR to the terms from the Plant Ontology developed by the Plant Ontology Consortium (POC, www.plantontology.org).</p>
<p><br>
6.TAIR10 or ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz)<br>
This file contains functional descriptions for gene models included in either the TAIR 10 or as of 20170630 the Araport11 genome release. TAIR10/Araport11 refers to the version of the genome annotation.<br>
</p>
<p>7.Araport11_GFF3_genes_transposons.[DATE].gff.gz</p>
<pre>8. Araport11_GFF3_genes_transposons.MMMYYYY.gff.gz
This document is a tab-delimited file in GFF format. This document contains annotations from Araport11 genome release. Annotations in this file include information curated from recent scientific literature.
Note: This file is available starting with the 20211231 Data Release.
Column header: explanation
1. Name of the chromosome
2. Source: Name of the the data source that generated this feature (Araport11)
3. Annotation type: eg gene, mRNA etc.
4. Start position of annotation.
5. Stop position of annotation.
6. Score - A floating point value.
7. Strand information. Defined as + (forward) or - (reverse).
8. Frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.
9. Detailed annotation information with a semicolon-separated list of tag-value pairs, providing additional information about each feature, including curator summary, computational description,. etc.
9. Araport11_GTF_genes_transposons.MMMYYYY.gtf.gz
This document is a tab-delimited file in GTF format. This document contains annotations from Araport11 genome release. Annotations in this file include information curated from recent scientific literature.
Note: This file is available starting with the 20211231 Data Release.
Column header: explanation
1. Name of the chromosome
2. Source: Name of the the data source that generated this feature (Araport11)
3. Annotation type: eg gene, mRNA etc.
4. Start position of annotation.
5. Stop position of annotation.
6. Score - A floating point value.
7. Strand information. Defined as + (forward) or - (reverse).
8. Frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.
9. Detailed annotation information with a semicolon-separated list of tag-value pairs, providing additional information about each feature, including transcript_id. gene_id, Note, etc. </pre>
TAIR functional annotation data
No full text<p>Quarterly release of curated gene function data for Arabidopsis thaliana from The Arabidopsis Information Resource (www.arabidopsis.org)</p>
<p>The contents of the compressed archive include the following files which are described in detail in the included README file.</p>
<p><br>
1.ATH_GO_GOSLIM.txt.gz<br>
This document is a tab-delimited file containing GO annotations for Arabidopsis genes annotated by TAIR and TIGR with terms from the Gene Ontology Consortium controlled vocabularies (see www.geneontology.org). This file includes an updated set of literature based annotations and >40,000 electronic annotations based upon matches to INTERPRO domains supplied by Nicola Mulder from SWISS PROT/INTERPRO. </p>
<p>Please cite this paper when using TAIR's GO annotations in your research: Berardini, TZ, Mundodi, S, Reiser, L, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11. </p>
<p><br>
2.gene_aliases_yyyymmdd.txt(.gz)<br>
This file lists alternative names for each gene.</p>
<p><br>
3.Locus_Germplasm_Phenotype_yyyymmdd.txt.gz<br>
This file contains links between loci, germplasms, and phenotypes. <br>
<br>
4.Locus_Published_yyyymmdd.txt.gz<br>
This file contains links between loci and publications. <br>
<br>
5.po_temporal_gene_arabidopsis_tair.assoc.gz<br>
po_anatomy_gene_arabidopsis_tair.assoc.gz<br>
These two files are tab-delimited files. Each contains the <br>
set of literature-based annotations of Arabidopsis genes and loci annotated at TAIR to the terms from the Plant Ontology developed by the Plant Ontology Consortium (POC, www.plantontology.org).</p>
<p><br>
6.TAIR10 or ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz)<br>
This file contains functional descriptions for gene models included in either the TAIR 10 or as of 20170630 the Araport11 genome release. TAIR10/Araport11 refers to the version of the genome annotation.<br>
</p>
<p>7.Araport11_GFF3_genes_transposons.[DATE].gff.gz</p>
<pre>8. Araport11_GFF3_genes_transposons.MMMYYYY.gff.gz
This document is a tab-delimited file in GFF format. This document contains annotations from Araport11 genome release. Annotations in this file include information curated from recent scientific literature.
Note: This file is available starting with the 20211231 Data Release.
Column header: explanation
1. Name of the chromosome
2. Source: Name of the the data source that generated this feature (Araport11)
3. Annotation type: eg gene, mRNA etc.
4. Start position of annotation.
5. Stop position of annotation.
6. Score - A floating point value.
7. Strand information. Defined as + (forward) or - (reverse).
8. Frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.
9. Detailed annotation information with a semicolon-separated list of tag-value pairs, providing additional information about each feature, including curator summary, computational description,. etc.
9. Araport11_GTF_genes_transposons.MMMYYYY.gtf.gz
This document is a tab-delimited file in GTF format. This document contains annotations from Araport11 genome release. Annotations in this file include information curated from recent scientific literature.
Note: This file is available starting with the 20211231 Data Release.
Column header: explanation
1. Name of the chromosome
2. Source: Name of the the data source that generated this feature (Araport11)
3. Annotation type: eg gene, mRNA etc.
4. Start position of annotation.
5. Stop position of annotation.
6. Score - A floating point value.
7. Strand information. Defined as + (forward) or - (reverse).
8. Frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.
9. Detailed annotation information with a semicolon-separated list of tag-value pairs, providing additional information about each feature, including transcript_id. gene_id, Note, etc. </pre>
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