TAIR functional annotation data

Quarterly 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.gzThis 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.gzThis file contains links between loci, germplasms, and phenotypes. 4.Locus_Published_yyyymmdd.txt.gzThis file contains links between loci and publications. 5.po_temporal_gene_arabidopsis_tair.assoc.gz6. po_anatomy_gene_arabidopsis_tair.assoc.gzThese 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). 7.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. 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.本数据集为拟南芥信息资源库（The Arabidopsis Information Resource，TAIR，官网：www.arabidopsis.org）发布的拟南芥（Arabidopsis thaliana）经人工整理注释的基因功能数据季度更新版本。 压缩归档包内包含以下文件，各文件的详细说明请参见附带的README文档。 1. ATH_GO_GOSLIM.txt.gz 该文件为制表符分隔的文本文件，包含由TAIR与TIGR注释的拟南芥基因的基因本体（Gene Ontology，GO）注释信息，所用术语来自基因本体联盟的受控词汇表（详见www.geneontology.org）。本文件包含更新后的基于文献的注释集，以及超过40000条基于SWISS-PROT/INTERPRO结构域匹配结果的电子注释，该匹配数据由Nicola Mulder提供。 若您在研究中使用TAIR的GO注释，请引用以下论文：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) 本文件列出了各基因的别名。 3. Locus_Germplasm_Phenotype_yyyymmdd.txt.gz 本文件包含基因座、种质与表型之间的关联关系。 4. Locus_Published_yyyymmdd.txt.gz 本文件包含基因座与已发表文献之间的关联关系。 5. po_temporal_gene_arabidopsis_tair.assoc.gz 6. po_anatomy_gene_arabidopsis_tair.assoc.gz 上述两个文件均为制表符分隔的文本文件，各自包含TAIR注释的拟南芥基因与基因座的基于文献的注释集，所用术语来自植物本体联盟（Plant Ontology Consortium，POC，官网：www.plantontology.org）开发的植物本体术语体系。 7. TAIR10 or ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz) 本文件包含TAIR10或截至2017年6月30日发布的Araport11基因组版本中的基因模型的功能描述信息。TAIR10/Araport11指代基因组注释的版本号。 8. Araport11_GFF3_genes_transposons.MMMYYYY.gff.gz 本文件为GFF格式的制表符分隔文本文件，包含Araport11基因组版本的注释信息，其中注释内容源自近期科学文献的人工整理注释。 注意：本文件自2021年12月31日数据发布版本起提供。 列标题及说明如下： 1. 染色体名称 2. 来源：生成该特征的数据源名称（即Araport11） 3. 注释类型：例如gene、mRNA等 4. 注释起始位置 5. 注释终止位置 6. 得分：浮点型数值 7. 链信息：定义为'+'（正向链）或'-'（反向链） 8. 读码框：取值为'0'、'1'或'2'。'0'表示该特征的第一个碱基为密码子的第一个碱基，'1'表示第二个碱基为密码子的第一个碱基，依此类推。 9. 详细注释信息：以分号分隔的标签-值对列表，用于提供每个特征的额外信息，包括注释员摘要、计算型描述等。 9. Araport11_GTF_genes_transposons.MMMYYYY.gtf.gz 本文件为GTF格式的制表符分隔文本文件，包含Araport11基因组版本的注释信息，其中注释内容源自近期科学文献的人工整理注释。 注意：本文件自2021年12月31日数据发布版本起提供。 列标题及说明如下： 1. 染色体名称 2. 来源：生成该特征的数据源名称（即Araport11） 3. 注释类型：例如gene、mRNA等 4. 注释起始位置 5. 注释终止位置 6. 得分：浮点型数值 7. 链信息：定义为'+'（正向链）或'-'（反向链） 8. 读码框：取值为'0'、'1'或'2'。'0'表示该特征的第一个碱基为密码子的第一个碱基，'1'表示第二个碱基为密码子的第一个碱基，依此类推。 9. 详细注释信息：以分号分隔的标签-值对列表，用于提供每个特征的额外信息，包括transcript_id、gene_id、Note等。