UniProt query

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Metanode that makes api calls to UniProtKB to retrieve selected data based on protein IDs. Protein IDs have to be in UniProt format, e.g. P12345 (https://www.uniprot.org/help/accession_numbers). Multiple protein IDs separated by delimiter (e.g. semicolon) are supported. You can ask to remove common prefix and or suffix to be removed prior quering the accession on the UniProtKB. Duplicate protein ID values (prior prefix/sufix removal) are removed prior api call.

Metanode retrieves query in tabular output form where one should select columns to be returned specifically. Please check UniProt help (https://www.uniprot.org/help/return_fields) for the full list of avaiable columns and use "Columns to retrieve" setting to adjust accordingly. Not correctly spelled column names are ignored and not present in the output table.

Two tables are returned by the metanode - top one containing individual protein IDs and specified columns retrieved from UniProt and bottom table containing accessions for which empty query result was retrieved (e.g. missing accessions).

You can specify output column names (as strings separated by comma ","), UniProt column names will be used as default values.

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Used programs and tools and their respective licenses at the time of the metanode creation. Version numbers and the licenses might differ based on your local installation. Please inspect your local installation and contact us if you can not locate your local version and or license terms.

KNIME nodes (The KNIME nodes consists of the following GNU GPL 3.0 License. Licence terms are available here: https://www.gnu.org/licenses/gpl.html)
Python 3 (The Python consists of the following Python 3.6 License. Licence terms are available here: https://docs.python.org/3.6/license.html)
Python package Pandas (The Pandas consists of the following BSD License. Licence terms are available here: https://opensource.org/licenses/BSD-3-Clause)

UniProt API (The UniProt API consists of the following Creative Commons Attribution (CC BY 4.0) License. Licence terms are available here: http://creativecommons.org/licenses/by/4.0/)

The metanode was created in KNIME 4.1.3. running inside the docker image (https://hub.docker.com/r/cfprot/knime/), tag 4.1.3a.

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This version of metanode is available under the GNU GPL 3.0 License, unless stated otherwise. The full version of the license terms is available at https://www.gnu.org/licenses/gpl.html.
Version: 0.4.1 from 2022-08-12
Contact person: David Potesil (david.potesil@ceitec.muni.cz)
More information can be found at https://github.com/OmicsWorkflows/KNIME_metanodes.

Options

Protein IDs column

column containing protein IDs to be searched for on UniProt

Protein IDs delimiter

delimiter used to divide individual IDs in Protein IDs column

Accessions prefix to remove

common prefix to be removed from all accessions, letters size matters; leave empty for no removal

Accessions suffix to remove

common suffix to be removed from all accessions, letters size matters; leave empty for no removal

Columns to retrieve

list of columns to retrieve from uniprot via their API provided as a list separated by comma ",".%%00010(you can use whitespaces, they are replaced by %20 later with string replacer node)

Output table ProteinID column name

column name to set for proteinID column after processing input column with protein ids

Output column names

column names as strings with comma "," used as a delimiter; eg. genes,entry name,interactor; if empty, column names retrieved from uniprot will be used

Nodes

• String Input6 ×
• Python Script (1⇒1)2 ×
• Chunk Loop Start1 ×
• Column Filter1 ×
• Column Rename1 ×
• Show all 14 nodes

Extensions

• FeatureKNIME Base nodes
• FeatureKNIME Javasnippet
• FeatureKNIME Python 2 Integration (legacy)
• FeatureKNIME Quick Forms
• FeatureKNIME REST Client Extension

Links

• No links available