Processing Uberon data

Uberon is "an integrated cross-species ontology … representing a variety of anatomical entities. [source]" We use Uberon as the vocabulary to represent anatomical structures for our drug repurposing research.

Execution

To reconstruct the analysis, run the notebooks in the following order:

human-constraint.ipynb: Compares two methods for filtering the ontology for anatomies that exist in humans.
process.ipynb: Downloads and processes the Uberon ontology in OBO format. Creates TSVs of terms, xrefs, and subsets. Additionally, creates Uberon hetio-slim, a subset of Uberon terms for inclusion in our hetnet.

Datasets

The following datasets are created:

terms.tsv: the identifiers and names of Uberon terms
subset.tsv: the ontology subsets for terms
xref.tsv: cross-references to external vocabularies
human-constraint.tsv: assessments of whether a term exists or not in humans based on two methods.
hetio-slim.tsv: the slim term set used for our drug repurposing project.

License

Uberon content and its derivatives are licensed under CC-BY. All original content in this repository is released as CC0.

human-constraint.ipynb: RecursionError: maximum recursion depth exceeded

An error occurred in the module below. I used the current version uberon 2021.02.13. But when I used the old version you provided 2015-07-24 Uberon release, there is no error.

The error message is:

---------------------------------------------------------------------------
RecursionError                            Traceback (most recent call last)
<ipython-input-9-8c5d22ff6c90> in <module>
      9     # Find whether term is in humans by seeing if node or its children
     10     # xref specific human terminologies
---> 11     children = get_children(ontology, node, in_keys = {'is_a', 'part_of', 'develops_from'})
     12     child_xrefs = set()
     13     for child in children | {node}:

<ipython-input-7-44d667171172> in get_children(graph, node, in_keys, out_keys)
      4         if key in in_keys:
      5             children.add(u)
----> 6             children |= get_children(graph, u)
      7     for u, v, key in graph.out_edges(node, keys=True):
      8         if key in out_keys:

... last 1 frames repeated, from the frame below ...

<ipython-input-7-44d667171172> in get_children(graph, node, in_keys, out_keys)
      4         if key in in_keys:
      5             children.add(u)
----> 6             children |= get_children(graph, u)
      7     for u, v, key in graph.out_edges(node, keys=True):
      8         if key in out_keys:

RecursionError: maximum recursion depth exceeded
-------------------------------------------------------------------------------------------------------

The error message was as follows, and I tried several things, but it didn't work. What should I do?

-------------------------------------------------------------------------------------------------------
import sys
sys.setrecursionlimit(30000)
print(sys.getrecursionlimit())
-------------------------------------------------------------------------------------------------------
The kernel for  human-constraint.ipynb appears to have died. It will restart automatically.
-------------------------------------------------------------------------------------------------------

Kindly regards

dhimmel / uberon Goto Github PK

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Processing Uberon data

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OBO Dependency

human-constraint.ipynb: RecursionError: maximum recursion depth exceeded

The error message is:

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