Renaming labels in NER

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#1

Hi,

I annotated a large amount of documents with very granular labels. Now, I want to merge some very granular labels in its "parent" label. Is there a way to edit label names in prodigy? I thought of a way to do this (stated below), but wanted to know if it can be done in Prodigy.

Method (prodigy->python->prodigy): Get the output of the database, edit "spans" in the output jsonl file via python. Read the jsonl as a new database into Prodigy.

Any help or recommendation is welcomed! Thanks!

Splitting labels in NER
#2

Hi! That sounds like a reasonable approach to me :slightly_smiling_face: Datasets in Prodigy are append-only by design, so you'd probably want to create a new dataset for your edited annotations. And if it turns out you want to go back to the previous state, you still have the old dataset available.

(If you're a jq wizard, you could probably write a command-line one-liner to do the data transformation and then pipe the result forward to a new dataset, all in one step. But I couldn't tell you how :sweat_smile:)

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#3

@ines there might be a bug in this process.

Here was my workflow:

  1. prodigy db-out dataset_granular_labels > granular_labels.jsonl
  2. In python, change "label" value to the less granular value for all annotations under "spans".
  3. In python, save it as less_granular.jsonl
    • Checked whether less_granular.jsonl contained the changed labels and it does.
  4. prodigy db-in dataset_lessgranular less_granular.jsonl

However when I do prodigy review dataset_lessgranular_reviewed dataset_lessgranular --label labels_less_granular.txt, I see the less granular labels (what I changed them to) on the top in the label choice section, but the existing labels (highlighted yellow in the text) are still the old ones.

Any recommendation would be appreciated!

============================== ✨  Prodigy Stats ==============================

Version          1.9.9
Platform         Windows-10-10.0.18362-SP0
Python Version   3.6.2
Database Name    SQLite
Database Id      sqlite
#4

Hmm, there's very little magic going on here and the review recipe should just show you whatever is in that datast :thinking: When you look at what's in your dataset_lessgranular dataset (e.g. using db-out), which labels do you see here and how many examples are in there? Maybe it somehow ended up with a copy of the previous unedited data?

#5
  • less_granular.jsonl: has the edited (less granular) labels. This is the altered db-out via python script.
  • After db-ining less_granular.jsonl, I db-outed it again as less_granular_prodigy.jsonl. I see the less granular version of the labels here too (under the main "spans"). However, under "versions", I see other "spans", that contain the granular labels. To visualize for one document:
{"text" : "..."
...
"tokens": [...]
"spans": [ LESS GRANULAR LABELS SEEN HERE ] 
"versions": [
       {"text" : "..."
         ...
         "tokens": [...]
         "spans": [ GRANULAR LABELS SEEN HERE ] 
         "versions": [
                {"text" : "..."
                  ...
                  "tokens": [...]
                  "spans": [ GRANULAR LABELS SEEN HERE TOO ] 
                }
       }
]
}
#6

Late to the party, but I've successfully changed labels just using sed.

sed 's,"label":"OLD_LABEL","label":"NEW_LABEL",g' old_task.jsonl > new_task.jsonl
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