2024-02-20

This is PMAS's COMMONS Lab daily Open Notebook.

Today is 2024.02.20

Todo today

Have a look at the COMMONS research discussion forum

- https://github.com/orgs/commons-research/discussions

Daily work on the Open Science for natural products research Viewpoint

See Viewpoint

Doing

Training Pascal

Dendron training with people.pascal-amrein (Private)

Shared https://doi.org/10.5281/zenodo.8137605

We'll work at https://github.com/orgs/commons-research/projects/2

MIBIG workshop

MiBIG workshop MIBIG started in 2015 https://mibig.secondarymetabolites.org/

Apparently had some notes over there Mibig

Interoperable with

npatlas
GNPS
Rhea

Launching MiBIG 4.0 3 annotathon rounds

Substantial contribution : actively participating in at least 2-hour annotathon sessions or equivalent (reviewing entries, writing)

MiBIG organization team Coordinators Interest groups

MIBIG 4.0 Data Standard

separate between biosynthesis vs. compound classification
use controlled vocabulary where possible
keep citations close to claims
keep related data points together
make parts of the schema reusable elsewhere
More DB cross links (e.g. MITE db) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y

operon

MITE minimum information about a tailoring enzyme/maturase

During this meeting, we will inform you about the scope and focus of the annotathons, some organizational improvements, and our upcoming MIBiG Online Submission system. We will also discuss the new roles of Coordinators and Reviewers in detail. Make sure to tune in!

We also want to announce the dates of the annotathons. Please bear in mind that for co-authorship on the next MIBiG publication, participation in at least two 3-hour annotathon sessions (or an equivalent contribution) is necessary. The MIBiG annotathon dates are:

• March 19th 7 am – 10 pm and 4 pm – 7 pm (GMT)
• April 23rd 7 am – 10 pm and 4 pm – 7 pm (GMT)
• May 14th 7 am – 10 pm and 4 pm – 7 pm (GMT)

Further, we want to make a call for contributions to our MIBiG Literature table (http://tinyurl.com/mibig-literature). In this table, we are collecting recent publications on biosynthetic gene cluster that are currently missing in the MIBiG database, but also publications that report additional information on already existing MIBiG entries. This collection of publications will be used as a starting point during the annotathons. If you have publications that you want to see covered during the annotathons, please feel free to add them to the table. We have prepared an explanatory document in case of any uncertainties (http://tinyurl.com/mibig-literature-explanation).

Colleagues who have indicated to be interested in acting as Coordinators or Reviewers will receive an additional email about these roles in the next few days.

We are looking forward to welcome you at the Kickoff meetings!

Kind regards,

Marnix Medema, Mitja Zdouc, and the MIBiG team

They mention the https://www.contributor-covenant.org/