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_TAGS for fine-grained tasks #703

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_TAGS for fine-grained tasks #703

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4aa3d84
add _TAGS
sg-wbi Jun 7, 2022
4f328b4
add _TAGS
sg-wbi Jun 7, 2022
515d9ac
create Tags Enum
sg-wbi Jun 7, 2022
beb1eb6
update _TAGS
sg-wbi Jun 8, 2022
9ebbdf4
new tags
sg-wbi Jun 8, 2022
02deb9a
add tags
sg-wbi Jun 8, 2022
5d42aeb
add tags
sg-wbi Jun 8, 2022
52c561d
new tags
sg-wbi Jun 8, 2022
14fff79
complete adding tags
sg-wbi Jun 8, 2022
71ceed5
ORGANISM is SPECIES, SOCIAL_MEDIA belongs to `source` not `subtask`
sg-wbi Jun 8, 2022
1b0b89e
rm ORGANISM
sg-wbi Jun 8, 2022
f5cc052
add DIAGNOSIS tag
sg-wbi Jun 8, 2022
f4b528e
add n2c2 datasets
sg-wbi Jun 8, 2022
fbfdc70
add diagnosis tag
sg-wbi Jun 8, 2022
7f96f08
update tags
sg-wbi Jun 8, 2022
4109ebf
format
sg-wbi Jun 8, 2022
a7728ab
add tags to examples
sg-wbi Jun 8, 2022
dda930f
fix missing/errors
sg-wbi Jun 8, 2022
3493d0f
treatment is procedure
sg-wbi Jun 8, 2022
44bce0c
add script to gather (fine-grained) tasks counts
sg-wbi Jun 8, 2022
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/an_em/an_em.py
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import bigbio.utils.parsing as parse
from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.ANATOMY]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/anat_em/anat_em.py
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import bigbio.utils.parsing as parsing
from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.ANATOMY]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/ask_a_patient/ask_a_patient.py
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Expand Up @@ -21,11 +21,12 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "ask_a_patient"

_TAGS = [Tags.ADR]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bc5cdr/bc5cdr.py
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Expand Up @@ -31,10 +31,11 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses
from bigbio.utils.parsing import get_texts_and_offsets_from_bioc_ann

_TAGS = [Tags.DISEASE, Tags.CHEMICAL]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bc7_litcovid/bc7_litcovid.py
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from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.COVID]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bio_sim_verb/bio_sim_verb.py
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from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

# TODO: Add BibTeX citation
_TAGS = [Tags.LEXICAL]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bio_simlex/bio_simlex.py
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from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

# TODO: Add BibTeX citation
_TAGS = [Tags.LEXICAL]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bioasq_2021_mesinesp/bioasq_2021_mesinesp.py
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Expand Up @@ -51,9 +51,10 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.DOCUMENT_INDEXING]
_LANGUAGES = [Lang.ES]
_PUBMED = False
_LOCAL = False
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9 changes: 8 additions & 1 deletion bigbio/biodatasets/bioasq_task_b/bioasq_task_b.py
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Expand Up @@ -32,9 +32,16 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [
Tags.YESNO,
Tags.FACTOID,
Tags.FACTOID_LIST,
Tags.ABSTRACTIVE,
Tags.EXTRACTIVE,
]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = True
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bioasq_task_c_2017/bioasq_task_c_2017.py
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Expand Up @@ -23,9 +23,10 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.GRANT]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = True
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bioinfer/bioinfer.py
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from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.PPI]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/biology_how_why_corpus/biology_how_why_corpus.py
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Expand Up @@ -30,9 +30,10 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.HOW, Tags.WHY]
_LANGUAGES = [Lang.EN]
_PUBMED = False
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/biomrc/biomrc.py
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from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.MULTIPLE_CHOICE, Tags.MRC, Tags.CLOZE_TEST]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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7 changes: 6 additions & 1 deletion bigbio/biodatasets/bionlp_shared_task_2009/bionlp_shared_task_2009.py
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Expand Up @@ -21,10 +21,15 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses
from bigbio.utils.parsing import brat_parse_to_bigbio_kb, parse_brat_file

# http://www.wikicfp.com/cfp/servlet/event.showcfp?eventid=4605&copyownerid=320
# Task 1. Event detection and characterization
# Task 2. Event argument recognition
# Task 3. Recognition of negations and speculations
_TAGS = [Tags.PPI, Tags.NEGATION, Tags.SPECULATION, Tags.GENE]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bionlp_st_2011_epi/bionlp_st_2011_epi.py
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Expand Up @@ -21,13 +21,14 @@

from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2011_epi"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [Tags.EPIGENETICS, Tags.NEGATION, Tags.SPECULATION, Tags.GENE]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bionlp_st_2011_ge/bionlp_st_2011_ge.py
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Expand Up @@ -20,13 +20,14 @@

from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2011_ge"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [Tags.NEGATION, Tags.SPECULATION, Tags.GENE]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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10 changes: 9 additions & 1 deletion bigbio/biodatasets/bionlp_st_2011_id/bionlp_st_2011_id.py
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Expand Up @@ -20,13 +20,21 @@

from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2011_id"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [
Tags.DISEASE,
Tags.GENE,
Tags.CHEMICAL,
Tags.SPECIES,
Tags.SPECULATION,
Tags.NEGATION,
]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bionlp_st_2011_rel/bionlp_st_2011_rel.py
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from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2011_rel"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [Tags.PART_OF, Tags.GENE]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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12 changes: 11 additions & 1 deletion bigbio/biodatasets/bionlp_st_2013_cg/bionlp_st_2013_cg.py
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Expand Up @@ -20,12 +20,22 @@

from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2013_cg"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [
Tags.DISEASE,
Tags.CANCER,
Tags.TISSUE,
Tags.SPECIES,
Tags.CELL,
Tags.GENE,
Tags.CHEMICAL,
Tags.PATHWAY_CURATION,
]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bionlp_st_2013_ge/bionlp_st_2013_ge.py
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from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2013_ge"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [Tags.NEGATION, Tags.SPECULATION, Tags.GENE]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bionlp_st_2013_gro/bionlp_st_2013_gro.py
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Expand Up @@ -21,13 +21,14 @@

from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2013_gro"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [Tags.GENE, Tags.SPECIES, Tags.CELL, Tags.TISSUE]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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9 changes: 8 additions & 1 deletion bigbio/biodatasets/bionlp_st_2013_pc/bionlp_st_2013_pc.py
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Expand Up @@ -20,12 +20,19 @@

from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2013_pc"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [
Tags.GENE,
Tags.CHEMICAL,
Tags.PATHWAY_CURATION,
Tags.NEGATION,
Tags.SPECULATION,
]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bionlp_st_2019_bb/bionlp_st_2019_bb.py
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from bigbio.utils import parsing, schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "bionlp_st_2019_bb"
_SOURCE_VIEW_NAME = "source"
_UNIFIED_VIEW_NAME = "bigbio"

_TAGS = [Tags.SPECIES]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/biored/biored.py
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Expand Up @@ -26,10 +26,11 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

# TODO: Add BibTeX citation
_TAGS = [Tags.GENE, Tags.DISEASE, Tags.CHEMICAL, Tags.VARIANT, Tags.PPI]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/biorelex/biorelex.py
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Expand Up @@ -35,10 +35,11 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

# TODO: Add BibTeX citation
_TAGS = [Tags.GENE, Tags.CHEMICAL, Tags.VARIANT, Tags.NEGATION, Tags.SPECULATION]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/bioscope/bioscope.py
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Expand Up @@ -35,9 +35,10 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_TAGS = [Tags.NEGATION, Tags.SPECULATION]
_LANGUAGES = [Lang.EN]
_PUBMED = True
_LOCAL = False
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3 changes: 2 additions & 1 deletion bigbio/biodatasets/biosses/biosses.py
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Expand Up @@ -28,11 +28,12 @@

from bigbio.utils import schemas
from bigbio.utils.configs import BigBioConfig
from bigbio.utils.constants import Lang, Tasks
from bigbio.utils.constants import Lang, Tags, Tasks
from bigbio.utils.license import Licenses

_DATASETNAME = "biosses"

_TAGS = [Tags.SENTENCE]
_LANGUAGES = [Lang.EN]
_PUBMED = False
_LOCAL = False
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