progenetix/oncopubs

Submission repository for articles to be included in the Progenetix publication collection of cancer genome profiling studies

oncopubs

oncopubs is the input repository to register publications for the progenetix collection.

Monitored technologies include:

• "cCGH" - Chromosomal based Comparative Genomic Hybridization (CGH)
• "aCGH" - genomic arrays, referring to two color CGH arrays as well as other genomic arrays suitable for reconstructing copy number aberration data (SNP arrays ...)
• "WES" - whole exome sequencing
• "WGS" - whole genome sequencing

The data is represented through the publications portal of the Progenetix website.

To contribute to the extension of this repository minimal data is required. PMID, number of samples and information about the technology used should be provided - please use the template file for submissions into the incoming directory.

All contributions will be reviewed by our group and then they will be included in our database.

Publication template file

The template file is provided as a tab-delimited data table. It can be opened in text editors or spreadheet software, but please make sure to save the edited file then again as tab-delimited file.

The order of the columns can be changed, but please do not modify the header values.

Data Columns

#

Any value here (but use #) skips this line during import (e.g. for example data, testing, keeping processed entries...).

pubmedid

The PMID, and only this.

counts.ccgh

Number of chromosomal CGH experiments in the publication.

counts.acgh

Number of genomic array experiments (full genome only, not focal!) in the publication.

counts.wes

Number of whole exome sequencing experiments in the publication.

counts.wgs

Number of whole exome sequencing experiments in the publication.

counts.genomes

Number of genomes analyzed in th estudy; this may be less than the sum from different technologies - e.g. a study using 100 arrays may include 10 WGS experiments of some of the samples, keeping the genomes count at 100.

contact.name

Name of (one of) the corresponding author(s). Optional.

contact.email

email of (one of) the corresponding author(s). Optional.

contact.affiliation

Institution of (one of) the corresponding author(s). Optional.

PROVENANCE_ID

The geo key used to identify the city of origin. This can be looked up using the bycon services API:

• use the URL https://progenetix.org/services/geolocations?output=text&city= with an added city / start of city name (e.g. New)
  • https://progenetix.org/services/geolocations?output=text&city=New
• scroll the response for the correct location & copy the id value
  • e.g. newcastleupontyne::unitedkingdom

status

The status is mostly for internal use, e.g. labeling publications as excluded [GWAS study] or such. One direct use case is the collection of articles which may not have original data but use the Progenetix resource (excluded [Progenetix use]).

SAMPLE_TYPES

This field is for adding information about the approximate diagnoses of the analyzed cancer samples using the NCIt neoplasm codes. The codes themselves can be retrieved through the Progenetix services API.

The format is __NCIT code__::__label__::__count__. If several tumor diagnoses are included one can use several of those "blocks" and concatenate them with a semicolon.

Example NCIT:C4917::Lung Small Cell Carcinoma::36;NCIT:C2926::Lung Non-Small Cell Carcinoma::86

If this is left empty we will try to update later.

note

For some comments - can be empty ...

progenetix_use

This is a special field to labe publications which have used or cited the Progenetix ecosystem to list them on a dedicated page.

The field should be left empty - or labeled yes in case of Progenetix use.

progenetix_curator

Name of the person providing the entry.

Progenetix publications update procedure (locally...)

To insert/update the Progenetix publications database one uses the publicationsInserter.py script from the byconeer package and points it to the local version of an updated publication table. The script will fetch the extended information for the PMIDs (authors, title, abstract ...), combine those with the table annotations and create database entries (which become immediately available online if run on the Progenetix server).

Example:

./publicationsInserter.py -i ~/Github/oncopubs/incoming/2022-01-13-genome-screening-articles.tsv

Options:

• -u 1 overwrites existing records with the same PMIDs, e.g. after adding/correcting annotations
• -t 1 activates a test mode (JSON of data is shown but not inserted)