INCATools / INCATools/ontology-access-kit

Reproducing the enrichment example from today's OBO tutorial

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Description

cc: @cmungall @matentzn

From this slide:

https://docs.google.com/presentation/d/1b714y5W9EdjypwrHKNdDT4liVqMIbsIDfGxxrVWFxc0/edit#slide=id.g215fddbc4d6_0_181

My understanding is that the code should be:

```bash
runoak -i sqlite:obo:mondo normalize -M OMIM .desc//p=i EDS | grep -v ^id > omim.txt
runoak -i sqlite:obo:hp enrichment -p i -U omim.txt
```
> PS: There is a typo in the presentation I think, the '-M' is not in capital

This gives me the following error when running `enrichment`:

```
AttributeError: 'NoneType' object has no attribute 'lookup'
```

My `omim.txt` file looks like this, not sure it's the right format:

```
OMIM:130020 None
OMIM:130050 None
OMIM:130060 None
OMIM:130090 None
OMIM:147900 None
OMIM:225310 None
OMIM:225320 None
OMIM:225410 None
OMIM:305200 None
OMIM:606408 None
OMIM:608763 None
OMIM:612350 None
OMIM:614170 None
OMIM:614557 None
OMIM:615349 None
OMIM:615539 None
OMIM:617174 None
OMIM:225400 None
OMIM:130000 None
OMIM:130010 None
OMIM:601776 None
OMIM:130070 None
OMIM:130080 None
OMIM:229200 None
OMIM:619115 None
OMIM:619120 None
OMIM:616471 None
OMIM:617821 None
OMIM:618000 None
```

Contributor guide

Open the contributing guide

Research direction

Start by running the two `runoak` commands from the issue and inspect the reported `NoneType` lookup failure in the `enrichment` entry point. Compare the generated `omim.txt` contents with the tutorial example; done means the commands run successfully with the expected input format.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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