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DO NOT MERGE YET :) example usage of data_var in pattern #481

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DO NOT MERGE YET :) example usage of data_var in pattern #481

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@srobb1 srobb1 commented Jun 18, 2019

changed

  • added data_var exact_syns
  • added data_var def_xrefs
  • generated synonymns
  • removed exact synonyms in the annotations block

Example TSV

defined_class defined_class_name anatomical_entity1 anatomical_entity1_label anatomical_entity2 anatomical_entity2_label exact_syns def_dbxrefs defined_class_exact_synonym
PLANA:1000032 PLANA:0000030 midline PLANA:0000030 midline syn1 | syn2 | syn3 PMID:0000000 | UBERON:00000000 test overwrite defined_class_exact_synonym

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example usage of data_var in pattern
9e081ad 
changed
 - exact_syns
 - def_xrefs
 - generated synonymns
 - removed exact synonyms in the annotations block

Example TSV
|               |                    |                    |                          |                    |                          |                     |                                |                                            | 
|---------------|--------------------|--------------------|--------------------------|--------------------|--------------------------|---------------------|--------------------------------|--------------------------------------------| 
| defined_class | defined_class_name | anatomical_entity1 | anatomical_entity1_label | anatomical_entity2 | anatomical_entity2_label | exact_syns          | def_dbxrefs                    | defined_class_exact_synonym                | 
| PLANA:1000032 |                    | PLANA:0000030      | midline                  | PLANA:0000030      | midline                  | syn1 \| syn2 \|  syn3 | PMID:0000000 \| UBERON:00000000 | test overwrite defined_class_exact_synonym |
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srobb1 commented Jun 18, 2019

make does fail if the columns are missing from the TSV :(

@matentzn matentzn mentioned this pull request Jun 18, 2019
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I made another ticket here: INCATools/dosdp-tools#137

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Thanks @srobb1 !!! :) Lets see what our generals advice.

@matentzn matentzn changed the title example usage of data_var in pattern DO NOT MERGE YET :) example usage of data_var in pattern Jun 23, 2019
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Note to self: Consolidate with https://github.com/FlyBase/drosophila-phenotype-ontology/blob/master/src/patterns/dosdp-patterns/dpoAbnormalEntityTestXref.yaml

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@srobb1 @matentzn