Shulou(Shulou.com)06/01 Report--

Today, I will talk to you about the platform information in the GEO database, which may not be well understood by many people. In order to make you understand better, the editor has summarized the following content for you. I hope you can get something according to this article.

The platform in the GEO database represents the sequencing platform or chip platform, and each platform is uniquely identified by a number beginning with GPL. For a platform, it usually contains the following three types of files

Soft

Miniml

Suppl

Take GPL20814 as an example, the link is as follows

Https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20814

Both soft and miniml represent the basic information of the platform, such as GPL number, upload date, etc. Parts of the soft file are as follows

^ DATABASE = GeoMiameplate DatabaseSecretname = Gene Expression Omnibus (GEO)! Database_institute = NCBI NLM NIHangDatabaseupload webpage link = http://www.ncbi.nlm.nih.gov/geo!Database_email = geo@ ncbi.nlm.nih.gov.hk ^ platform = GPL20814 platform platform title = Human miRNA Array miRbase release 1900 platform geotechnical status = Public on Jun 12 2017 platform format replacement date = Aug 18 2015 platform format lastworthy updatedate = Jun 12 2017

In the soft file, the information for each category begins with ^, and the common categories are as follows

DATABASE

PLATFORM

SAMPLE

SERIES

DATABASE represents the basic information of the GEO database, PLATFORM represents the basic information of the platform, SAMPLE represents the sample information obtained by the platform, and SERIES represents a set of samples obtained using the platform.

In each category,! The beginning represents a type of information, and the general format is key = value, such as

Platform_geo_accession = GPL20814

For the chip platform, it will also provide information such as the corresponding relationship between probes and genes. On the corresponding web page, we can see the following table.

This section also exists in the soft file, as shown below

! platform_table_beginID Reporter Name miRNA_ID SPOT_ID272 hsa-miR-99b-5p MIMAT0000689 271 hsa-miR-99b-3p MIMAT0004678 270 hsa-miR-99a-5p MIMAT0000097 269 hsa-miR-99a-3p MIMAT0004511 268 hsa-miR-98-5p MIMAT0000096.

Use the paired two! Exclamation marks to indicate the beginning and end of the data, storing the corresponding table data in the middle.

The content in miniml is the same as soft, except that the above information is stored in XML format, while supplement file is a supplementary file uploaded by the submitter himself, with no clear format.

After reading the above, do you have any further understanding of the platform information in the GEO database? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.