Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

Scott Federhen; Karen Clark; Tanya Barrett; Helen Parkinson; James Ostell; Yuichi Kodama; Jun Mashima; Yasukazu Nakamura; Guy Cochrane; Ilene Karsch-Mizrachi

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Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

机译：迈向更丰富的微生物序列元数据：用BioProject，BioSample和Assembly记录替换菌株级NCBI分类学标本

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Microbial genome sequence submissions to the International Nucleotide Sequence Database Collaboration (INSDC) have been annotated with organism names that include the strain identifier. Each of these strain-level names has been assigned a unique ‘taxid’ in the NCBI Taxonomy Database. With the significant growth in genome sequencing, it is not possible to continue with the curation of strain-level taxids. In January 2014, NCBI will cease assigning strain-level taxids. Instead, submitters are encouraged provide strain information and rich metadata with their submission to the sequence database, BioProject and BioSample.

机译：向国际核苷酸序列数据库合作组织（INSDC）提交的微生物基因组序列已用包括菌株标识符的生物名称进行了注释。在NCBI分类数据库中，每个应变级别名称都被分配了一个唯一的“ taxid”。随着基因组测序的显着增长，不可能继续进行菌株水平的出租车。 2014年1月，NCBI将停止分配应变级别的出租车。相反，鼓励提交者在提交给序列数据库BioProject和BioSample的过程中提供菌株信息和丰富的元数据。

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《Standards in Genomic Sciences》 |2014年第3期|共页
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Scott Federhen; Karen Clark; Tanya Barrett; Helen Parkinson; James Ostell; Yuichi Kodama; Jun Mashima; Yasukazu Nakamura; Guy Cochrane; Ilene Karsch-Mizrachi;
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1. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata [J] . Eugene Gribov, Eugene Yaschenko, Ilene Karsch-Mizrachi, Nucleic acids research . 2012,第D1期

机译：NCBI的BioProject和BioSample数据库：促进元数据的捕获和组织
2. DNA SEQUENCING AND COMPARATIVE SEQUENCE ANALYSIS REVEAL THAT THE ESCHERICHIA COLI GENOMIC DNA MAY REPLACE THE TARGET DNA DURING MOLECULAR CLONING - EVIDENCE FOR THE ERRONEOUS ASSEMBLY OF E-COLI DNA INTO DATABASE SEQUENCES [J] . Jha PK., Sarkar S. Comparative biochemistry and physiology, Part B. Biochemistry & molecular biology . 1997,第2期

机译：DNA测序和比较序列分析表明，大肠埃希氏菌基因组DNA可能在分子克隆过程中取代目标DNA-证据表明E-Coli DNA已错误地组装到数据库序列中
3. “METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI’s sequence read archive” [J] . Mariam Qui?ones, David T. Liou, Conrad Shyu, BMC Bioinformatics . 2020,第1期

机译：“MetageNote：一个简化的网站标注基因组样本的网站平台，并简化到NCBI序列读取存档的提交”
4. Efforts to Link Ecological Metadata with Bacterial Gene Sequences at the Sapelo Island Microbial Observatory [C] . Wade M. SHELDON, Mary Ann MORAN, James T. HOLLIBAUGH World Multiconference on Systemics, Cybernetics and Informatics(SCI 2002) v.7: Information Systems Development II; 20020714-20020718; Orlando,FL; US . 2002

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5. Dynamics of agricultural soil fungi: Impact of agricultural land management on soil microbial biomass, fungal taxonomic richness and ligninolytic gene distribution. [D] . Wright, Christopher Allison. 2015

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6. Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject BioSample and Assembly records [O] . Scott Federhen, Karen Clark, Tanya Barrett, 2014

机译：迈向更丰富的微生物序列元数据：用BioProjectBioSample和Assembly记录代替菌株级NCBI分类法
7. Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records [O] . Scott Federhen, Karen Clark, Tanya Barrett, 2014

机译：迈向更丰富的微生物序列元数据：用BioProject，BioSample和Assembly记录代替菌株级NCBI分类法

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

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