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.拟南芥信息资源库（The Arabidopsis Information Resource，简称TAIR，www.arabidopsis.org）发布的经人工审编的拟南芥（Arabidopsis thaliana）基因功能数据季度更新包。 该压缩归档文件包含以下文件，各文件的详细说明见随附的README文档。 1. ATH_GO_GOSLIM.txt.gz：本文件为制表符分隔格式的文本文件，收录了由TAIR与TIGR完成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）。本文件包含经文献更新的注释集，以及由SWISS-PROT/INTERPRO的Nicola Mulder提供的、基于INTERPRO结构域匹配结果生成的逾40000条电子注释。 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：本文件收录了基因座、种质与表型之间的关联信息。 4. Locus_Published_yyyymmdd.txt.gz：本文件收录了基因座与已发表文献之间的关联信息。 5. po_temporal_gene_arabidopsis_tair.assoc.gz；6. po_anatomy_gene_arabidopsis_tair.assoc.gz：此两份文件均为制表符分隔格式的文本文件，分别收录了TAIR完成注释的、与植物本体联盟（Plant Ontology Consortium，简称POC，www.plantontology.org）开发的植物本体（Plant Ontology，PO）术语相关的拟南芥基因及基因座的文献基注释集。 7. TAIR10或ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz)：本文件收录了TAIR 10基因组注释版本，或截至2017年6月30日发布的Araport11基因组版本中所包含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，收录了Araport11基因组发布版本的注释信息，其中包含经近期科学文献审编的注释内容。注意：本文件自2021年12月31日数据发布起提供。 列标题及说明如下： 1. 染色体名称 2. 来源：生成该特征的数据来源名称（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. 分值：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，以此类推 9. 详细注释信息：以分号分隔的标签-值对列表，提供各特征的附加信息，包括审编人员摘要、计算描述等。 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，收录了Araport11基因组发布版本的注释信息，其中包含经近期科学文献审编的注释内容。注意：本文件自2021年12月31日数据发布起提供。 列标题及说明如下： 1. 染色体名称 2. 来源：生成该特征的数据来源名称（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. 分值：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，以此类推 9. 详细注释信息：以分号分隔的标签-值对列表，提供各特征的附加信息，包括transcript_id、gene_id、注释说明等。