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--- |
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tags: |
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- spacy |
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- token-classification |
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language: |
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- en |
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widget: |
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- text: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the coronavirus disease-19 (COVID-19) pandemic, was identified in late 2019 and caused >5 million deaths by February 2022. To date, targeted antiviral interventions against COVID-19 are limited. The spectrum of SARS-CoV-2 infection ranges from asymptomatic to fatal disease. However, the reasons for varying outcomes to SARS-CoV-2 infection are yet to be elucidated. Here we show that an endogenously activated interferon lambda (IFN位1) pathway leads to resistance against SARS-CoV-2 infection." |
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- text: "The NHS is offering antibody and antiviral treatments to people with coronavirus (COVID-19) who are at highest risk of becoming seriously ill." |
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model-index: |
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- name: en_covid19_ner |
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results: |
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- task: |
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name: NER |
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type: token-classification |
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metrics: |
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- name: NER Precision |
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type: precision |
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value: 0.9139786332 |
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- name: NER Recall |
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type: recall |
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value: 0.9362022309 |
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- name: NER F Score |
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type: f_score |
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value: 0.9249569618 |
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--- |
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COVID 19 Bio Annotations |
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The dataset was taken from https://github.com/davidcampos/covid19-corpus |
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Dataset |
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The dataset was then split into several datasets each one representing one entity. Namely, Disorder, Species, Chemical or Drug, Gene and Protein, Enzyme, Anatomy, Biological Process, Molecular Function, Cellular Component, Pathway and microRNA. Moreover, another dataset is also created with all those aforementioned that are non-overlapping in nature. |
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Other Dataset Formats |
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The datasets are available in two formats IOB and Spacy's JSONL format. |
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IOB: https://github.com/tsantosh7/COVID-19-Named-Entity-Recognition/tree/master/Datasets/BIO |
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SpaCy JSONL: https://github.com/tsantosh7/COVID-19-Named-Entity-Recognition/tree/master/Datasets/SpaCy |
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| Feature | Description | |
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| --- | --- | |
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| **Name** | `en_covid19_ner` | |
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| **Version** | `0.0.0` | |
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| **spaCy** | `>=3.2.4,<3.3.0` | |
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| **Default Pipeline** | `transformer`, `ner` | |
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| **Components** | `transformer`, `ner` | |
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| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) | |
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| **Sources** | n/a | |
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| **License** | n/a | |
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| **Author** | [Santosh Tirunagai]() | |
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### Label Scheme |
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<details> |
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<summary>View label scheme (10 labels for 1 components)</summary> |
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| Component | Labels | |
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| --- | --- | |
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| **`ner`** | `ANAT`, `CHED`, `COMP`, `DISO`, `ENZY`, `FUNC`, `PATH`, `PRGE`, `PROC`, `SPEC` | |
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</details> |
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### Accuracy |
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| Type | Score | |
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| --- | --- | |
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| `ENTS_F` | 92.50 | |
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| `ENTS_P` | 91.40 | |
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| `ENTS_R` | 93.62 | |
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| `TRANSFORMER_LOSS` | 311768.03 | |
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| `NER_LOSS` | 371171.50 | |
