TODO: Perform OWL Reasoner Evaluation about pheknowlator HOT 18 OPEN

Noon is great!

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Current status of attempting to use Konclude though the OWL-API is summarized here: ignazio1977/owllink-owlapi#2

Probably not worth meeting today unless you have something you want to discuss.

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Yep, let's meet. I should have some preliminary data to show you.

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@bill-baumgartner - I won't be able to meet during our normal Wednesday time, but can meet anytime today after 1pm and anytime tomorrow (for the most part). Let me know that works best for you!

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Evaluation steps look good. What was the result of ./owltools -h?
I can meet @ 1pm today. Tomorrow looks dicey due to the weather forecast.

from pheknowlator.

Evaluation steps look good. What was the result of ./owltools -h?
I can meet @ 1pm today. Tomorrow looks dicey due to the weather forecast.

I have something at 1pm. I could do 12pm or 2pm. Do either of those work?

The result of running ./owltools -h indicated that of our list of potential ontologies, only ELK and Pellet were included.

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@bill-baumgartner - following up from our meeting yesterday. Can you please take a look at OWLTools to see how difficult it might be to add a reasoner from the OWLAPI? Thank you!!

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@callahantiff - can you post the list of reasoners we selected?

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@callahantiff - can you post the list of reasoners we selected?

No problem, @bill-baumgartner the reasoners we chose are shown in the table below.

from pheknowlator.

First pass - the biggest issue is that most of the available reasoners support OWL API v3, and not v4 or v5.

• elephant - C code, "Support for OWL API is planned"
• pellet - OWL API v3
• racer - OWL API v3
• chainsaw - OWL API v3
• konclude - no direct connect to OWL API, but may be possible to use: https://www.derivo.de/en/products/konclude/usage-owl-api/
• crack - listed as unmaintained here: http://owl.cs.manchester.ac.uk/tools/list-of-reasoners/
• trowl - OWL API v3
• more - OWL API v3

• fact++ - supports OWL API v4
• snorocket - not on our list, but supports OWL API v4

I'll take a look at integrating Konclude first as it looks to be doable, and then perhaps we take a closer look and prioritize the rest.

from pheknowlator.

First pass - the biggest issue is that most of the available reasoners support OWL API v3, and not v4 or v5.

• elephant - C code, "Support for OWL API is planned"

• pellet - OWL API v3

• racer - OWL API v3

• chainsaw - OWL API v3

• konclude - no direct connect to OWL API, but may be possible to use: https://www.derivo.de/en/products/konclude/usage-owl-api/

• crack - listed as unmaintained here: http://owl.cs.manchester.ac.uk/tools/list-of-reasoners/

• trowl - OWL API v3

• more - OWL API v3

• fact++ - supports OWL API v4

• snorocket - not on our list, but supports OWL API v4

I'll take a look at integrating Konclude first as it looks to be doable, and then perhaps we take a closer look and prioritize the rest.

Thanks for the update @bill-baumgartner! I think your plan sounds great! Let me know if I can do anything in the meantime! I will also be in tomorrow if you prefer to meet in person.

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@bill-baumgartner - did you want to touch base on this stuff today?

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Turns out that Konclude works well from the command-line (in conjunction with Docker). So far I have not figured out how to retrieve explanations for unsatisfiable classes, but it is straightforward to:

• check the consistency of an ontology, e.g.
  docker run --rm --name "konclude" -v /local/path/to/ontologies:/data konclude/konclude consistency -i /data/cl.owl
• classify an ontology, e.g.
  docker run --rm --name "konclude" -v /local/path/to/ontologies:/data konclude/konclude classify -v -i /data/cl.owl -o /data/cl.konclude.out
• and, check the satisfiability of a specific class, e.g.
  docker run --rm --name "konclude" -v /local/path/to/ontologies:/data konclude/konclude satisfiability -v -i /data/cl.owl -x http://purl.obolibrary.org/obo/CL_2000096

from pheknowlator.

Turns out that Konclude works well from the command-line (in conjunction with Docker). So far I have not figured out how to retrieve explanations for unsatisfiable classes, but it is straightforward to:

• check the consistency of an ontology, e.g.
  docker run --rm --name "konclude" -v /local/path/to/ontologies:/data konclude/konclude consistency -i /data/cl.owl
• classify an ontology, e.g.
  docker run --rm --name "konclude" -v /local/path/to/ontologies:/data konclude/konclude classify -v -i /data/cl.owl -o /data/cl.konclude.out
• and, check the satisfiability of a specific class, e.g.
  docker run --rm --name "konclude" -v /local/path/to/ontologies:/data konclude/konclude satisfiability -v -i /data/cl.owl -x http://purl.obolibrary.org/obo/CL_2000096

Awesome, thanks Bill! Once I have the graph built I will give this a try! Happy to help dig around to find the output for unsatisfiable classes too.

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Morning @bill-baumgartner!

Below is a link to download a zipped directory of the ontologies we can use for the reasoner challenge. I have spent the last few days extensively cleaning these files (i.e. removed punning, fixing erroneous Literal typing, correcting inconsistent imported ontology identifiers, etc.). I also went ahead and ran each cleaned file through ELK to make sure that the cleaning didn't inadvertently cause other errors. All of them passed.

Download Link: reasoner_challenge.zip

Directory Contents
Aside from the clean single ontology files, you will also find:

• Each individual, cleaned ontology (n=10)
• A file for each pairwise ontology merge (n=45; naming scheme: ont1_ont2_merged.owl)
• A file of all of the single ontologies merged together (all_ontologies_merged.owl)

Note. All ontologies in the directory contain all original entities (i.e. not had all annotation assertions removed to create the minimal symbolic representation). I figured we should start with them intact and if need be, apply the reduction transformation later on (it's super easy to do).

Question: @bill-baumgartner - do we want all triple-, quad-, ...n-1-wise merge files? It is easy to generate these, but thought I would ask just in case you had something else in mind.

Ok, that's all for now, see you in a few hours! 😄 🎉

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@bill-baumgartner - here is the Jupyter Notebook I mentioned during our meeting today (incase you are curious).

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@bill-baumgartner - just wanted to check-in and see how the great reasoner challenge of 2020 was going? Still OK to meet at our usual time tomorrow?

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Yep, let's meet. I should have some preliminary data to show you.

@bill-baumgartner - Woo hoo! Sounds great, I am looking forward to it!

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