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Diffstat (limited to 'topics/data-uploads')
| -rw-r--r-- | topics/data-uploads/data_dictionaries_20230222.txt.zip | bin | 0 -> 2437 bytes | |||
| -rw-r--r-- | topics/data-uploads/gn-uploader-requirements.gmi | 32 |
2 files changed, 16 insertions, 16 deletions
diff --git a/topics/data-uploads/data_dictionaries_20230222.txt.zip b/topics/data-uploads/data_dictionaries_20230222.txt.zip Binary files differnew file mode 100644 index 0000000..5a8ba2f --- /dev/null +++ b/topics/data-uploads/data_dictionaries_20230222.txt.zip diff --git a/topics/data-uploads/gn-uploader-requirements.gmi b/topics/data-uploads/gn-uploader-requirements.gmi index 8a1bfcd..871cf99 100644 --- a/topics/data-uploads/gn-uploader-requirements.gmi +++ b/topics/data-uploads/gn-uploader-requirements.gmi @@ -52,9 +52,9 @@ and for data in ProbeSetData, it would be something like: We can then have table indexes composed of one or more of the elements of the *FULL IDENTIFIER* for faster queries. -**NOTE 01**: The *FULL IDENTIFIERS* above should be hieararchical, beginning with the "oldest" ancestor and ending with the current record's ID. +**NOTE 01**: The FULL IDENTIFIERS above should be hieararchical, beginning with the "oldest" ancestor and ending with the current record's ID. -**NOTE 02**: The examples of the *FULL IDENTIFIERS* above might not be complete. I'll update them as I tease more information from the database. +**NOTE 02**: The examples of the FULL IDENTIFIERS above might not be complete. I'll update them as I tease more information from the database. ## Data Categories @@ -115,14 +115,14 @@ Hierarchy We could index the genotype information by the following fields: * SpeciesId: For faster queries for a particular species' genotypes -* … +* ... ### Assembly Information * mm8 * mm10 * mm11 -* … +* ... etc. I still do not wholly comprehend this. This might be related to the platform information. @@ -135,7 +135,7 @@ Tables affected by this information: * Geno * Chr_Length -* … +* ... ### Population Information @@ -167,7 +167,7 @@ The data we need to collect/have for the samples are: From the existing `Strain` table, it seems you can only have one-and-only-one sample for a particular species with a specific name. > MariaDB [db_webqtl]> SHOW CREATE TABLE Strain; -> … +> ... > | Strain | CREATE TABLE `Strain` ( > `Id` int(20) NOT NULL AUTO_INCREMENT, > `Name` varchar(100) DEFAULT NULL, @@ -179,7 +179,7 @@ From the existing `Strain` table, it seems you can only have one-and-only-one sa > UNIQUE KEY `Name` (`Name`,`SpeciesId`), > KEY `Symbol` (`Symbol`) > ) ENGINE=InnoDB AUTO_INCREMENT=180927 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci | -> … +> ... We could index this information by any one, or combinations of the following fields: @@ -191,7 +191,7 @@ and maybe even drop the need for the 'StrainXRef' table. (*To be considered*) ### Tissue Information Hierarchy -> Species --> ?? … ?? --> Tissue --> {{{ data of various sorts }}} +> Species --> ?? ... ?? --> Tissue --> {{{ data of various sorts }}} Felix discovered the need for this when uploading the Arabidopsis Thaliana data into the test database with the uploader. Expression data to be uploaded has to be linked to a tissue, and the existing tissue information (as of before 2024-02-22T09:45+03:00UTC) seems to only belong to vertebrates, not plants. @@ -205,15 +205,15 @@ Tables: * TissueProbeSetFreeze * TissueProbeSetXRef -… +... ### Expression Data Information Hierarchy -> Species --> ?? … ?? --> Expression Data --> {{{ data of various sorts }}} +> Species --> ?? ... ?? --> Expression Data --> {{{ data of various sorts }}} -The ' --> ?? … ?? --> ' section winds through Platform, Population, Genotype, Tissue, Samples etc before making its way to the expression data information. I still need to unwind the hieararchy and list the paths here. +The ' --> ?? ... ?? --> ' section winds through Platform, Population, Genotype, Tissue, Samples etc before making its way to the expression data information. I still need to unwind the hieararchy and list the paths here. Affects the following database tables: @@ -228,18 +228,18 @@ Some mandatory data we need: * SpeciesId (see 'Species Information' above) * PlatformId (see 'Platform Information' above) * Name: Phenotype identifier for the platform above -* Gene Symbol: … +* Gene Symbol: ... * Chromosome: * Megabases: * Description: A description for the phenotype * GeneId: Entrez gene ID from NCBI * Strand_Gene/Strand_Probe: he DNA strand (+ or -) of the gene assigned to the phenotype. Leading or lagging strand. -Maybe the *Chromosome* and *Megabases* value could be replaced by a single link to a ChromosomeId or such… maybe a table linking the chromosome to its specific assembly e.g. +Maybe the *Chromosome* and *Megabases* value could be replaced by a single link to a ChromosomeId or such... maybe a table linking the chromosome to its specific assembly e.g. > Probeset(ChromosomeAssemblyId) --> (Id)ChromosomeAssembly(ChromosomeId) --> Chromosome(Id) -… +... ### Publish Phenotype Data @@ -262,9 +262,9 @@ Some important data required: * Units: Units of measurement for the phenotype => https://info.genenetwork.org/faq.php#q-22 Description for "Publish Phenotypes" -* Others? … +* Others? ... -… +... ## Descriptions |