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forestbiotech-lab / sRNA-Portal-workflow

The plant sRNA portal is an online resource integrating a workflow for identifying, predicting and annotating plant small RNAs (sRNA), and a database to store sRNA datasets with standardized metadata. The workflow (miRPursuit) is based on publicly available tools and allows the automated sequential application of data processing modules for analysis of sRNA datasets, including data preprocessing, filtering, annotation and reporting output. Additionally, tools for downstream analysis, such as expression matrix and prediction of sRNA target genes are integrated in the workflow. The database will work as a repository of the miRPursuit annotated sRNAs and other publicly available sRNAs, focusing mainly on woody plant data.
https://sRNA-portal.biodata.pt
GNU General Public License v3.0
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Add Organisms #1

Open netbofia opened 6 years ago

netbofia commented 6 years ago

Add Organisms into SQL.

netbofia commented 6 years ago

Where to get the common name from?

A) Leave empty and fill afterwards B) Try to get it from NCBI taxon?

netbofia commented 6 years ago
To accomplish this go through the pseudo API

https://www.ebi.ac.uk/ols/api/ontologies/ncbitaxon/terms?iri=http://purl.obolibrary.org/obo/NCBITaxon_3702 curl this with the ncbi_id

Search in array obo_synonym for the first name with type “common name” or related