Datasets:

Languages:
English
License:
system HF staff commited on
Commit
453edc3
1 Parent(s): 1e4e4dc

Update files from the datasets library (from 1.12.0)

Browse files

Release notes: https://github.com/huggingface/datasets/releases/tag/1.12.0

Files changed (3) hide show
  1. README.md +32 -7
  2. dataset_infos.json +1 -1
  3. linnaeus.py +1 -1
README.md CHANGED
@@ -18,6 +18,7 @@ task_categories:
18
  task_ids:
19
  - named-entity-recognition
20
  paperswithcode_id: linnaeus
 
21
  ---
22
 
23
  # Dataset Card for [Dataset Name]
@@ -56,21 +57,27 @@ paperswithcode_id: linnaeus
56
 
57
  ### Dataset Summary
58
 
59
- [More Information Needed]
60
 
61
  ### Supported Tasks and Leaderboards
62
 
63
- [More Information Needed]
64
 
65
  ### Languages
66
 
67
- [More Information Needed]
68
 
69
  ## Dataset Structure
70
 
71
  ### Data Instances
72
 
73
- [More Information Needed]
 
 
 
 
 
 
74
 
75
  ### Data Fields
76
 
@@ -80,7 +87,10 @@ paperswithcode_id: linnaeus
80
 
81
  ### Data Splits
82
 
83
- [More Information Needed]
 
 
 
84
 
85
  ## Dataset Creation
86
 
@@ -138,7 +148,22 @@ paperswithcode_id: linnaeus
138
 
139
  ### Citation Information
140
 
141
- [More Information Needed]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
142
  ### Contributions
143
 
144
- Thanks to [@edugp](https://github.com/edugp) for adding this dataset.
 
18
  task_ids:
19
  - named-entity-recognition
20
  paperswithcode_id: linnaeus
21
+ pretty_name: LINNAEUS
22
  ---
23
 
24
  # Dataset Card for [Dataset Name]
 
57
 
58
  ### Dataset Summary
59
 
60
+ LINNAEUS is a general-purpose dictionary matching software, capable of processing multiple types of document formats in the biomedical domain (MEDLINE, PMC, BMC, OTMI, text, etc.). It can produce multiple types of output (XML, HTML, tab-separated-value file, or save to a database). It also contains methods for acting as a server (including load balancing across several servers), allowing clients to request matching over a network. A package with files for recognizing and identifying species names is available for LINNAEUS, showing 94% recall and 97% precision compared to LINNAEUS-species-corpus.
61
 
62
  ### Supported Tasks and Leaderboards
63
 
64
+ This dataset is used for species Named Entity Recognition.
65
 
66
  ### Languages
67
 
68
+ The dataset is in English.
69
 
70
  ## Dataset Structure
71
 
72
  ### Data Instances
73
 
74
+ An example from the dataset is:
75
+
76
+ ```
77
+ {'id': '2',
78
+ 'tokens': ['Scp160p', 'is', 'a', '160', 'kDa', 'protein', 'in', 'the', 'yeast', 'Saccharomyces', 'cerevisiae', 'that', 'contains', '14', 'repeats', 'of', 'the', 'hnRNP', 'K', '-', 'homology', '(', 'KH', ')', 'domain', ',', 'and', 'demonstrates', 'significant', 'sequence', 'homology', 'to', 'a', 'family', 'of', 'proteins', 'collectively', 'known', 'as', 'vigilins', '.'],
79
+ 'ner_tags': [0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]}
80
+ ```
81
 
82
  ### Data Fields
83
 
 
87
 
88
  ### Data Splits
89
 
90
+
91
+ | name |train|validation|test|
92
+ |----------|----:|---------:|---:|
93
+ | linnaeus |11936| 4079|7143|
94
 
95
  ## Dataset Creation
96
 
 
148
 
149
  ### Citation Information
150
 
151
+ ```bibtex
152
+ @article{Gerner2010,
153
+ abstract = {The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.},
154
+ author = {Gerner, Martin and Nenadic, Goran and Bergman, Casey M},
155
+ doi = {10.1186/1471-2105-11-85},
156
+ issn = {1471-2105},
157
+ journal = {BMC Bioinformatics},
158
+ number = {1},
159
+ pages = {85},
160
+ title = {{LINNAEUS: A species name identification system for biomedical literature}},
161
+ url = {https://doi.org/10.1186/1471-2105-11-85},
162
+ volume = {11},
163
+ year = {2010}
164
+ }
165
+ ```
166
+
167
  ### Contributions
168
 
169
+ Thanks to [@edugp](https://github.com/edugp) for adding this dataset.
dataset_infos.json CHANGED
@@ -1 +1 @@
1
- {"linnaeus": {"description": "A novel corpus of full-text documents manually annotated for species mentions.\n", "citation": "@article{gerner2010linnaeus,\n title={LINNAEUS: a species name identification system for biomedical literature},\n author={Gerner, Martin and Nenadic, Goran and Bergman, Casey M},\n journal={BMC bioinformatics},\n volume={11},\n number={1},\n pages={85},\n year={2010},\n publisher={Springer}\n}\n", "homepage": "http://linnaeus.sourceforge.net/", "license": "", "features": {"id": {"dtype": "string", "id": null, "_type": "Value"}, "tokens": {"feature": {"dtype": "string", "id": null, "_type": "Value"}, "length": -1, "id": null, "_type": "Sequence"}, "ner_tags": {"feature": {"num_classes": 3, "names": ["O", "B", "I"], "names_file": null, "id": null, "_type": "ClassLabel"}, "length": -1, "id": null, "_type": "Sequence"}}, "post_processed": null, "supervised_keys": null, "builder_name": "linnaeus", "config_name": "linnaeus", "version": {"version_str": "1.0.0", "description": null, "major": 1, "minor": 0, "patch": 0}, "splits": {"train": {"name": "train", "num_bytes": 4772417, "num_examples": 11936, "dataset_name": "linnaeus"}, "validation": {"name": "validation", "num_bytes": 1592823, "num_examples": 4079, "dataset_name": "linnaeus"}, "test": {"name": "test", "num_bytes": 2802877, "num_examples": 7143, "dataset_name": "linnaeus"}}, "download_checksums": {"https://drive.google.com/u/0/uc?id=1OletxmPYNkz2ltOr9pyT0b0iBtUWxslh&export=download/": {"num_bytes": 18204624, "checksum": "30522c752fd90e6da05f117a52da13174b246e4980e46840e6e1737dc67e1d27"}}, "download_size": 18204624, "post_processing_size": null, "dataset_size": 9168117, "size_in_bytes": 27372741}}
 
1
+ {"linnaeus": {"description": "A novel corpus of full-text documents manually annotated for species mentions.\n", "citation": "@article{gerner2010linnaeus,\n title={LINNAEUS: a species name identification system for biomedical literature},\n author={Gerner, Martin and Nenadic, Goran and Bergman, Casey M},\n journal={BMC bioinformatics},\n volume={11},\n number={1},\n pages={85},\n year={2010},\n publisher={Springer}\n}\n", "homepage": "http://linnaeus.sourceforge.net/", "license": "", "features": {"id": {"dtype": "string", "id": null, "_type": "Value"}, "tokens": {"feature": {"dtype": "string", "id": null, "_type": "Value"}, "length": -1, "id": null, "_type": "Sequence"}, "ner_tags": {"feature": {"num_classes": 3, "names": ["O", "B", "I"], "names_file": null, "id": null, "_type": "ClassLabel"}, "length": -1, "id": null, "_type": "Sequence"}}, "post_processed": null, "supervised_keys": null, "builder_name": "linnaeus", "config_name": "linnaeus", "version": {"version_str": "1.0.0", "description": null, "major": 1, "minor": 0, "patch": 0}, "splits": {"train": {"name": "train", "num_bytes": 4772417, "num_examples": 11936, "dataset_name": "linnaeus"}, "validation": {"name": "validation", "num_bytes": 1592823, "num_examples": 4079, "dataset_name": "linnaeus"}, "test": {"name": "test", "num_bytes": 2802877, "num_examples": 7143, "dataset_name": "linnaeus"}}, "download_checksums": {"https://drive.google.com/u/0/uc?id=1OletxmPYNkz2ltOr9pyT0b0iBtUWxslh&export=download": {"num_bytes": 18204624, "checksum": "30522c752fd90e6da05f117a52da13174b246e4980e46840e6e1737dc67e1d27"}}, "download_size": 18204624, "post_processing_size": null, "dataset_size": 9168117, "size_in_bytes": 27372741}}
linnaeus.py CHANGED
@@ -42,7 +42,7 @@ A novel corpus of full-text documents manually annotated for species mentions.
42
  """
43
 
44
  _HOMEPAGE = "http://linnaeus.sourceforge.net/"
45
- _URL = "https://drive.google.com/u/0/uc?id=1OletxmPYNkz2ltOr9pyT0b0iBtUWxslh&export=download/"
46
  _BIOBERT_NER_DATASET_DIRECTORY = "linnaeus"
47
  _TRAINING_FILE = "train.tsv"
48
  _DEV_FILE = "devel.tsv"
 
42
  """
43
 
44
  _HOMEPAGE = "http://linnaeus.sourceforge.net/"
45
+ _URL = "https://drive.google.com/u/0/uc?id=1OletxmPYNkz2ltOr9pyT0b0iBtUWxslh&export=download"
46
  _BIOBERT_NER_DATASET_DIRECTORY = "linnaeus"
47
  _TRAINING_FILE = "train.tsv"
48
  _DEV_FILE = "devel.tsv"