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In describing DNA assembly reactions, it would be useful to have a specific term for ligation of sequences.

It seems appropriate that this should be a child of SBO:conversion (SBO:0000182), as ligation is a modification of covalent bonds. It is also complementary with SBO:cleavage (SBO:0000178), which is the rupture of a covalent bond, whereas ligation is the formation of a covalent bond. It is also closely related to SBO:polymerization (SBO:0000652), except that refers to the joining of monomers to form a polymer whereas ligation is the joining of two or more polymers to form a larger polymer

Accordingly, I propose the following:

• Name: ligation
• Definition: Formation of a covalent bond resulting in the creation of a link between the ends of one or more linear polymer molecules.
• Parent: SBO:conversion (SBO:0000182)

Note that this definition of ligation can apply not only to DNA ligation but also the RNA ligation and protein ligation. This definition also allows for ligation to describe circularization of a single DNA fragment, joining of two DNA fragments, and joining of multiple DNA fragments.

In modelling stress in plants, we have abiotic factors (such as drought, heat, etc) precipitating the response.

Although SBO is one of the ontologies included on http://www.ontobee.org/, term lookup via the Ontobee search engine is no longer working there.

For example, searching for dissociation, which should find SBO:0000180, does not include it in the search results.

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

When validating SBML files from biomodels, we get the following warning whenever a species is annotated as messenger RNA:

• The value of the 'sboTerm' attribute on a <species> is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, "participant physical type"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, "material entity").
  Reference: L2V4 Section 5
  SBO term 'SBO:0000278' on the <species> is not in the appropriate branch.

It's possible that this is a validation problem, but I do think that messenger RNA is indeed a material entity (as well as being a 'functional entity'), and should be cross-added to that branch (like 'gene' is).

Dear SBO team,

The link for the Ontology Lookup Service on the main page of this GitHub repository seems to be outdated.

'SBO terms can be browsed through the Ontology Lookup Service (OLS) webpage https://www.ebi.ac.uk/ols/ontologies/sbo.

It leads me to a site with the message:
Something went wrong! Please contact [email protected] to report any bugs or give feedback.

Cause unknown (no exception details available)

This should be a quick fix and would improve the user experience a lot.

Thanks and best,

Sebastian

SBO:cleavage (SBO:0000178) is currently defined as "Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities."

For molecules with more complex topologies, however, cleavage may change the topology of the molecule without actually separating it into more than one entity. For example, a single cleavage of a circular DNA molecule results in a linear DNA molecule (and likewise for conversion of circular to linear proteins).

I would therefore propose to slightly generalize the definition to "Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities or into a physical entity of a different topological class."

wget http://purl.obolibrary.org/obo/sbo.owl

Results in a 404:

--2022-07-31 12:50:01--  http://purl.obolibrary.org/obo/sbo.owl
Resolving purl.obolibrary.org (purl.obolibrary.org)... 3.223.180.112
Connecting to purl.obolibrary.org (purl.obolibrary.org)|3.223.180.112|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://www.ebi.ac.uk/sbo/exports/Main/SBO_OWL.owl [following]
--2022-07-31 12:50:01--  http://www.ebi.ac.uk/sbo/exports/Main/SBO_OWL.owl
Resolving www.ebi.ac.uk (www.ebi.ac.uk)... 193.62.193.80
Connecting to www.ebi.ac.uk (www.ebi.ac.uk)|193.62.193.80|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.ebi.ac.uk/sbo/exports/Main/SBO_OWL.owl [following]
--2022-07-31 12:50:01--  https://www.ebi.ac.uk/sbo/exports/Main/SBO_OWL.owl
Connecting to www.ebi.ac.uk (www.ebi.ac.uk)|193.62.193.80|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2022-07-31 12:50:02 ERROR 404: Not Found.

You should change the PURL config if you want to redirect it to a different file:

https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/sbo.yml