WARNING:root:Could not find any mappings for fplx:Interferon

[suyanpengzhang]

I'm trying to follow the example provided in Strategy 1: Knowledge extraction using SPIRES

in command line I used: ontogpt extract -t gocam.GoCamAnnotations -i gocam-betacat.txt

But I got this warning: WARNING:root:Could not find any mappings for fplx:Interferon

Then the error message pops up:

Traceback (most recent call last): File "/Users/suyanpengzhang/opt/anaconda3/bin/ontogpt", line 8, in sys.exit(main()) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(*args, **kwargs) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/ontogpt/cli.py", line 337, in extract write_extraction(results, output, output_format, ke) File "/Users/suyanpengzhang/opt/anaconda3/lib/python3.9/site-packages/ontogpt/cli.py", line 107, in write_extraction output.write(dump_minimal_yaml(results).encode("utf-8")) TypeError: write() argument must be str, not bytes

[caufieldjh]

Hi @suyanpengzhang - thanks for trying out OntoGPT! The newest version (0.3.3) should fix the TypeError problem for you - please try updating and let me know if the error persists.

For this one: But I got this warning: WARNING:root:Could not find any mappings for fplx:Interferon this isn't really an error that is likely to impact results, but rather an instance in which a term was found that ontogpt couldn't find a better identifier for (specifically, using the NodeNormalizer tool). That makes sense here because the input definitely includes the term interferon but this could resolve to several different identifiers.