1,720,976 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 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 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 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>
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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