update

bigbiohub.py

@@ -1,65 +1,15 @@
-import json
 from collections import defaultdict
-from enum import Enum
-from types import SimpleNamespace
-from typing import Dict, Optional
-
 from dataclasses import dataclass
+from enum import Enum
 import datasets
 from datasets.utils.download_manager import DownloadManager
+from types import SimpleNamespace
 
+from .languages_data import LANGUAGES_DATA
+from .licenses import Licenses
 
-BigBioValues = SimpleNamespace(NULL="<BB_NULL_STR>")
-DL_MANAGER = DownloadManager()
-
-LANGUAGES_JSON_PATH = DL_MANAGER.download('https://huggingface.co/datasets/bigscience-biomedical/scitail/raw/main/languages.json')
-LICENSES_JSON_PATH = DL_MANAGER.download('https://huggingface.co/datasets/bigscience-biomedical/scitail/raw/main/licenses.json')
-
-@dataclass
-class License:
-    """
-    Base class from which all licenses inherit
-
-    Args:
-        name: License title
-        text: Accompanying information of the license
-        link: URL to License
-        version: Current version of license
-        provenance: Organization providing authorization, if possible
-    """
-
-    name: Optional[str] = None
-    short_name: Optional[str] = None
-    text: Optional[str] = None
-    link: Optional[str] = None
-    version: Optional[str] = None
-    provenance: Optional[str] = None
-
-    @property
-    def is_share_alike(self):
-        """
-        Is Share-alike?
-        """
-        # NOTE: leave here has an example of license properties
-        raise NotImplementedError()
-
-
-@dataclass
-class CustomLicense(License):
-    """
-    This class is for custom licenses.
-    It must contain the text of the license.
-    Optionally its version and a link to the license webpage.
-    """
-
-    def __post_init__(self):
-        if self.name is None:
-            self.name = "Custom license"
 
-        if self.text is None and self.link is None:
-            raise ValueError(
-                "A `CustomLicense` must provide either (a) the license text or (b) the license link!"
-            )
+BigBioValues = SimpleNamespace(NULL="<BB_NULL_STR>")
 
 
 @dataclass
@@ -75,20 +25,10 @@ class BigBioConfig(datasets.BuilderConfig):
 
 # shamelessly compied from:
 # https://github.com/huggingface/datasets/blob/master/src/datasets/utils/metadata.py
-langs_json = json.load(open(LANGUAGES_JSON_PATH, "r"))
-langs_dict = {k.replace("-", "_").upper(): v for k, v in langs_json.items()}
+langs_dict = {k.replace("-", "_").upper(): v for k, v in LANGUAGES_DATA.items()}
 Lang = Enum("Lang", langs_dict)
 
 
-METADATA: dict = {
-    "_LOCAL": bool,
-    "_LANGUAGES": Lang,
-    "_PUBMED": bool,
-    "_LICENSE": License,
-    "_DISPLAYNAME": str,
-}
-
-
 class Tasks(Enum):
     NAMED_ENTITY_RECOGNITION = "NER"
     NAMED_ENTITY_DISAMBIGUATION = "NED"
@@ -256,278 +196,3 @@ SCHEMA_TO_FEATURES = {
     "TEXT": text_features,
     "PAIRS": pairs_features,
 }
-
-
-
-
-
-def _get_variable_name(k: str) -> str:
-
-    return k.replace("-", "_").upper().replace(".", "p").replace("+", "plus")
-
-
-_GENIA_PROJECT_LICENSE_TEXT = """
-GENIA Project License for Annotated Corpora
-
-1. Copyright of abstracts
-
-Any abstracts contained in this corpus are from PubMed(R), a database
-of the U.S. National Library of Medicine (NLM).
-
-NLM data are produced by a U.S. Government agency and include works of
-the United States Government that are not protected by U.S. copyright
-law but may be protected by non-US copyright law, as well as abstracts
-originating from publications that may be protected by U.S. copyright
-law.
-
-NLM assumes no responsibility or liability associated with use of
-copyrighted material, including transmitting, reproducing,
-redistributing, or making commercial use of the data. NLM does not
-provide legal advice regarding copyright, fair use, or other aspects
-of intellectual property rights. Persons contemplating any type of
-transmission or reproduction of copyrighted material such as abstracts
-are advised to consult legal counsel.
-
-2. Copyright of full texts
-
-Any full texts contained in this corpus are from the PMC Open Access
-Subset of PubMed Central (PMC), the U.S. National Institutes of Health
-(NIH) free digital archive of biomedical and life sciences journal
-literature.
-
-Articles in the PMC Open Access Subset are protected by copyright, but
-are made available under a Creative Commons or similar license that
-generally allows more liberal redistribution and reuse than a
-traditional copyrighted work. Please refer to the license of each
-article for specific license terms.
-
-3. Copyright of annotations
-
-The copyrights of annotations created in the GENIA Project of Tsujii
-Laboratory, University of Tokyo, belong in their entirety to the GENIA
-Project.
-
-4. Licence terms
-
-Use and distribution of abstracts drawn from PubMed is subject to the
-PubMed(R) license terms as stated in Clause 1.
-
-Use and distribution of full texts is subject to the license terms
-applying to each publication.
-
-Annotations created by the GENIA Project are licensed under the
-Creative Commons Attribution 3.0 Unported License. To view a copy of
-this license, visit http://creativecommons.org/licenses/by/3.0/ or
-send a letter to Creative Commons, 444 Castro Street, Suite 900,
-Mountain View, California, 94041, USA.
-
-Annotations created by the GENIA Project must be attributed as
-detailed in Clause 5.
-
-5. Attribution
-
-The GENIA Project was founded and led by prof. Jun'ichi Tsujii and
-the project and its annotation efforts have been coordinated in part
-by Nigel Collier, Yuka Tateisi, Sang-Zoo Lee, Tomoko Ohta, Jin-Dong
-Kim, and Sampo Pyysalo.
-
-For a complete list of the GENIA Project members and contributors,
-please refer to http://www.geniaproject.org.
-
-The GENIA Project has been supported by Grant-in-Aid for Scientific
-Research on Priority Area "Genome Information Science" (MEXT, Japan),
-Grant-in-Aid for Scientific Research on Priority Area "Systems
-Genomics" (MEXT, Japan), Core Research for Evolutional Science &
-Technology (CREST) "Information Mobility Project" (JST, Japan),
-Solution Oriented Research for Science and Technology (SORST) (JST,
-Japan), Genome Network Project (MEXT, Japan) and Grant-in-Aid for
-Specially Promoted Research (MEXT, Japan).
-
-Annotations covered by this license must be attributed as follows:
-
-    Corpus annotations (c) GENIA Project
-
-Distributions including annotations covered by this licence must
-include this license text and Attribution section.
-
-6. References
-
-- GENIA Project : http://www.geniaproject.org
-- PubMed : http://www.pubmed.gov/
-- NLM (United States National Library of Medicine) : http://www.nlm.nih.gov/
-- MEXT (Ministry of Education, Culture, Sports, Science and Technology) : http://www.mext.go.jp/
-- JST (Japan Science and Technology Agency) : http://www.jst.go.jp
-"""
-
-GeniaProjectLicense = CustomLicense(
-    name="GENIA Project License for Annotated Corpora",
-    # NOTE: just in case the link will break
-    text=_GENIA_PROJECT_LICENSE_TEXT,
-    link="http://www.nactem.ac.uk/meta-knowledge/GENIA_license.txt",
-)
-
-
-_NLM_LICENSE_TEXT = """
-National Library of Medicine Terms and Conditions
-
-INTRODUCTION
-
-Downloading data from the National Library of Medicine FTP servers indicates your acceptance of the following Terms and Conditions: No charges, usage fees or royalties are paid to NLM for this data.
-
-GENERAL TERMS AND CONDITIONS
-
-    Users of the data agree to:
-        acknowledge NLM as the source of the data by including the phrase "Courtesy of the U.S. National Library of Medicine" in a clear and conspicuous manner,
-        properly use registration and/or trademark symbols when referring to NLM products, and
-        not indicate or imply that NLM has endorsed its products/services/applications.
-
-    Users who republish or redistribute the data (services, products or raw data) agree to:
-        maintain the most current version of all distributed data, or
-        make known in a clear and conspicuous manner that the products/services/applications do not reflect the most current/accurate data available from NLM.
-
-    These data are produced with a reasonable standard of care, but NLM makes no warranties express or implied, including no warranty of merchantability or fitness for particular purpose, regarding the accuracy or completeness of the data. Users agree to hold NLM and the U.S. Government harmless from any liability resulting from errors in the data. NLM disclaims any liability for any consequences due to use, misuse, or interpretation of information contained or not contained in the data.
-
-    NLM does not provide legal advice regarding copyright, fair use, or other aspects of intellectual property rights. See the NLM Copyright page.
-
-    NLM reserves the right to change the type and format of its machine-readable data. NLM will take reasonable steps to inform users of any changes to the format of the data before the data are distributed via the announcement section or subscription to email and RSS updates.
-
-"""
-NLMLicense = CustomLicense(
-    name="National Library of Medicine Terms and Conditions",
-    # NOTE: just in case the link will break
-    text=_NLM_LICENSE_TEXT,
-    link="https://www.nlm.nih.gov/databases/download/terms_and_conditions.html",
-)
-
-
-_PHYSIONET_LICENSE_1p5_TEXT = """
-The PhysioNet Credentialed Health Data License
-Version 1.5.0
-
-Copyright (c) 2022 MIT Laboratory for Computational Physiology
-
-The MIT Laboratory for Computational Physiology (MIT-LCP) wishes to make data available for research and educational purposes to qualified requestors, but only if the data are used and protected in accordance with the terms and conditions stated in this License.
-
-It is hereby agreed between the data requestor, hereinafter referred to as the "LICENSEE", and MIT-LCP, that:
-
-    The LICENSEE will not attempt to identify any individual or institution referenced in PhysioNet restricted data.
-    The LICENSEE will exercise all reasonable and prudent care to avoid disclosure of the identity of any individual or institution referenced in PhysioNet restricted data in any publication or other communication.
-    The LICENSEE will not share access to PhysioNet restricted data with anyone else.
-    The LICENSEE will exercise all reasonable and prudent care to maintain the physical and electronic security of PhysioNet restricted data.
-    If the LICENSEE finds information within PhysioNet restricted data that he or she believes might permit identification of any individual or institution, the LICENSEE will report the location of this information promptly by email to PHI-report@physionet.org, citing the location of the specific information in question.
-    The LICENSEE will use the data for the sole purpose of lawful use in scientific research and no other.
-    The LICENSEE will be responsible for ensuring that he or she maintains up to date certification in human research subject protection and HIPAA regulations.
-    The LICENSEE agrees to contribute code associated with publications arising from this data to a repository that is open to the research community.
-    This agreement may be terminated by either party at any time, but the LICENSEE's obligations with respect to PhysioNet data shall continue after termination.
-
-THE DATA ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DATA OR THE USE OR OTHER DEALINGS IN THE DATA.
-"""
-PhysioNetLicense1p5 = CustomLicense(
-    name="PhysioNet Credentialed Health Data License",
-    version="1.5",
-    link="https://physionet.org/content/mimiciv/view-license/0.4/",
-    # NOTE: just in case the link will break
-    text=_PHYSIONET_LICENSE_1p5_TEXT,
-)
-
-
-UMLSLicense = CustomLicense(
-    name="UMLS - Metathesaurus License Agreement",
-    link="https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html",
-)
-
-_NCBI_LICENSE_TEXT = """
-===========================================================================
-*
-*                            PUBLIC DOMAIN NOTICE
-*               National Center for Biotechnology Information
-*
-*  This software/database is a "United States Government Work" under the
-*  terms of the United States Copyright Act.  It was written as part of
-*  the author's official duties as a United States Government employee and
-*  thus cannot be copyrighted.  This software/database is freely available
-*  to the public for use. The National Library of Medicine and the U.S.
-*  Government have not placed any restriction on its use or reproduction.
-*
-*  Although all reasonable efforts have been taken to ensure the accuracy
-*  and reliability of the software and data, the NLM and the U.S.
-*  Government do not and cannot warrant the performance or results that
-*  may be obtained by using this software or data. The NLM and the U.S.
-*  Government disclaim all warranties, express or implied, including
-*  warranties of performance, merchantability or fitness for any particular
-*  purpose.
-*
-*  Please cite the author in any work or product based on this material.
-*
-*
-===========================================================================
-"""
-NCBILicense = CustomLicense(
-    name="National Center fr Biotechnology Information PUBLIC DOMAIN NOTICE",
-    link="https://github.com/openbiocorpora/genetag/blob/master/LICENSE",
-    # NOTE: just in case link will break
-    text=_NCBI_LICENSE_TEXT,
-)
-
-PublicDomainMark_1p0 = CustomLicense(
-    name="Public Domain Mark 1.0",
-    text="""This work has been identified as being free of known restrictions under copyright law,
-    including all related and neighboring rights.
-    """,
-    link="https://creativecommons.org/publicdomain/mark/1.0/",
-)
-
-
-def load_json_licenses() -> Dict[str, str]:
-    """
-    Load all licenses from JSON file.
-    Amend names to be valid variable names
-    """
-
-    # shamelessly compied from:
-    # https://github.com/huggingface/datasets/blob/master/src/datasets/utils/metadata.py
-    licenses = {
-        _get_variable_name(k): v
-        for k, v in json.loads(
-            open(LICENSES_JSON_PATH, "r").read()
-        ).items()
-    }
-
-    licenses["ZERO_BSD"] = licenses.pop("0BSD")
-
-    return licenses
-
-
-def load_licenses() -> Dict[str, License]:
-    """
-    Load `_LICENSES` dict:
-        - key (str) : license name
-        - value (License) : instance of license class
-    """
-
-    json_licenses = load_json_licenses()
-
-    json_licenses.update({"DUA": "Data User Agreement"})
-
-    licenses_kwargs = {k: {"name": v} for k, v in json_licenses.items()}
-
-    licenses = {k: License(**kwargs) for k, kwargs in licenses_kwargs.items()}
-
-    custom_licenses = {
-        "PUBLIC_DOMAIN_MARK_1p0": PublicDomainMark_1p0,
-        "GENIA_PROJECT_LICENSE": GeniaProjectLicense,
-        "NLM_LICENSE": NLMLicense,
-        "NCBI_LICENSE": NCBILicense,
-        "UMLS_LICENSE": UMLSLicense,
-        "PHYSIONET_LICENSE_1p5": PhysioNetLicense1p5,
-    }
-
-    licenses.update(custom_licenses)
-    for k, v in licenses.items():
-        v.short_name = k
-
-    return licenses
-
-
-_LICENSES = load_licenses()
-Licenses = SimpleNamespace(**_LICENSES)

biosses.py

@@ -28,8 +28,9 @@ import pandas as pd
 
 from .bigbiohub import pairs_features
 from .bigbiohub import BigBioConfig
-from .bigbiohub import Lang, Tasks
+from .bigbiohub import Lang
 from .bigbiohub import Licenses
+from .bigbiohub import Tasks
 
 
 _DATASETNAME = "biosses"

languages.json → languages_data.py

@@ -1,4 +1,4 @@
-{
+LANGUAGES_DATA = {
     "af": "Afrikaans",
     "af-NA": "Afrikaans (Namibia)",
     "af-ZA": "Afrikaans (South Africa)",
@@ -788,5 +788,5 @@
     "zh-Hant-MO": "Chinese (Traditional, Macao SAR China)",
     "zh-Hant-TW": "Chinese (Traditional, Taiwan)",
     "zu": "Zulu",
-    "zu-ZA": "Zulu (South Africa)"
-}
+    "zu-ZA": "Zulu (South Africa)",
+}

licenses.py

@@ -0,0 +1,318 @@
+from dataclasses import dataclass
+from typing import Dict, Optional
+from types import SimpleNamespace
+from .licenses_data import LICENSES_DATA
+
+
+@dataclass
+class License:
+    """
+    Base class from which all licenses inherit
+
+    Args:
+        name: License title
+        text: Accompanying information of the license
+        link: URL to License
+        version: Current version of license
+        provenance: Organization providing authorization, if possible
+    """
+
+    name: Optional[str] = None
+    short_name: Optional[str] = None
+    text: Optional[str] = None
+    link: Optional[str] = None
+    version: Optional[str] = None
+    provenance: Optional[str] = None
+
+    @property
+    def is_share_alike(self):
+        """
+        Is Share-alike?
+        """
+        # NOTE: leave here has an example of license properties
+        raise NotImplementedError()
+
+
+@dataclass
+class CustomLicense(License):
+    """
+    This class is for custom licenses.
+    It must contain the text of the license.
+    Optionally its version and a link to the license webpage.
+    """
+
+    def __post_init__(self):
+        if self.name is None:
+            self.name = "Custom license"
+
+        if self.text is None and self.link is None:
+            raise ValueError(
+                "A `CustomLicense` must provide either (a) the license text or (b) the license link!"
+            )
+
+
+_GENIA_PROJECT_LICENSE_TEXT = """
+GENIA Project License for Annotated Corpora
+
+1. Copyright of abstracts
+
+Any abstracts contained in this corpus are from PubMed(R), a database
+of the U.S. National Library of Medicine (NLM).
+
+NLM data are produced by a U.S. Government agency and include works of
+the United States Government that are not protected by U.S. copyright
+law but may be protected by non-US copyright law, as well as abstracts
+originating from publications that may be protected by U.S. copyright
+law.
+
+NLM assumes no responsibility or liability associated with use of
+copyrighted material, including transmitting, reproducing,
+redistributing, or making commercial use of the data. NLM does not
+provide legal advice regarding copyright, fair use, or other aspects
+of intellectual property rights. Persons contemplating any type of
+transmission or reproduction of copyrighted material such as abstracts
+are advised to consult legal counsel.
+
+2. Copyright of full texts
+
+Any full texts contained in this corpus are from the PMC Open Access
+Subset of PubMed Central (PMC), the U.S. National Institutes of Health
+(NIH) free digital archive of biomedical and life sciences journal
+literature.
+
+Articles in the PMC Open Access Subset are protected by copyright, but
+are made available under a Creative Commons or similar license that
+generally allows more liberal redistribution and reuse than a
+traditional copyrighted work. Please refer to the license of each
+article for specific license terms.
+
+3. Copyright of annotations
+
+The copyrights of annotations created in the GENIA Project of Tsujii
+Laboratory, University of Tokyo, belong in their entirety to the GENIA
+Project.
+
+4. Licence terms
+
+Use and distribution of abstracts drawn from PubMed is subject to the
+PubMed(R) license terms as stated in Clause 1.
+
+Use and distribution of full texts is subject to the license terms
+applying to each publication.
+
+Annotations created by the GENIA Project are licensed under the
+Creative Commons Attribution 3.0 Unported License. To view a copy of
+this license, visit http://creativecommons.org/licenses/by/3.0/ or
+send a letter to Creative Commons, 444 Castro Street, Suite 900,
+Mountain View, California, 94041, USA.
+
+Annotations created by the GENIA Project must be attributed as
+detailed in Clause 5.
+
+5. Attribution
+
+The GENIA Project was founded and led by prof. Jun'ichi Tsujii and
+the project and its annotation efforts have been coordinated in part
+by Nigel Collier, Yuka Tateisi, Sang-Zoo Lee, Tomoko Ohta, Jin-Dong
+Kim, and Sampo Pyysalo.
+
+For a complete list of the GENIA Project members and contributors,
+please refer to http://www.geniaproject.org.
+
+The GENIA Project has been supported by Grant-in-Aid for Scientific
+Research on Priority Area "Genome Information Science" (MEXT, Japan),
+Grant-in-Aid for Scientific Research on Priority Area "Systems
+Genomics" (MEXT, Japan), Core Research for Evolutional Science &
+Technology (CREST) "Information Mobility Project" (JST, Japan),
+Solution Oriented Research for Science and Technology (SORST) (JST,
+Japan), Genome Network Project (MEXT, Japan) and Grant-in-Aid for
+Specially Promoted Research (MEXT, Japan).
+
+Annotations covered by this license must be attributed as follows:
+
+    Corpus annotations (c) GENIA Project
+
+Distributions including annotations covered by this licence must
+include this license text and Attribution section.
+
+6. References
+
+- GENIA Project : http://www.geniaproject.org
+- PubMed : http://www.pubmed.gov/
+- NLM (United States National Library of Medicine) : http://www.nlm.nih.gov/
+- MEXT (Ministry of Education, Culture, Sports, Science and Technology) : http://www.mext.go.jp/
+- JST (Japan Science and Technology Agency) : http://www.jst.go.jp
+"""
+
+GeniaProjectLicense = CustomLicense(
+    name="GENIA Project License for Annotated Corpora",
+    # NOTE: just in case the link will break
+    text=_GENIA_PROJECT_LICENSE_TEXT,
+    link="http://www.nactem.ac.uk/meta-knowledge/GENIA_license.txt",
+)
+
+
+_NLM_LICENSE_TEXT = """
+National Library of Medicine Terms and Conditions
+
+INTRODUCTION
+
+Downloading data from the National Library of Medicine FTP servers indicates your acceptance of the following Terms and Conditions: No charges, usage fees or royalties are paid to NLM for this data.
+
+GENERAL TERMS AND CONDITIONS
+
+    Users of the data agree to:
+        acknowledge NLM as the source of the data by including the phrase "Courtesy of the U.S. National Library of Medicine" in a clear and conspicuous manner,
+        properly use registration and/or trademark symbols when referring to NLM products, and
+        not indicate or imply that NLM has endorsed its products/services/applications.
+
+    Users who republish or redistribute the data (services, products or raw data) agree to:
+        maintain the most current version of all distributed data, or
+        make known in a clear and conspicuous manner that the products/services/applications do not reflect the most current/accurate data available from NLM.
+
+    These data are produced with a reasonable standard of care, but NLM makes no warranties express or implied, including no warranty of merchantability or fitness for particular purpose, regarding the accuracy or completeness of the data. Users agree to hold NLM and the U.S. Government harmless from any liability resulting from errors in the data. NLM disclaims any liability for any consequences due to use, misuse, or interpretation of information contained or not contained in the data.
+
+    NLM does not provide legal advice regarding copyright, fair use, or other aspects of intellectual property rights. See the NLM Copyright page.
+
+    NLM reserves the right to change the type and format of its machine-readable data. NLM will take reasonable steps to inform users of any changes to the format of the data before the data are distributed via the announcement section or subscription to email and RSS updates.
+
+"""
+NLMLicense = CustomLicense(
+    name="National Library of Medicine Terms and Conditions",
+    # NOTE: just in case the link will break
+    text=_NLM_LICENSE_TEXT,
+    link="https://www.nlm.nih.gov/databases/download/terms_and_conditions.html",
+)
+
+
+_PHYSIONET_LICENSE_1p5_TEXT = """
+The PhysioNet Credentialed Health Data License
+Version 1.5.0
+
+Copyright (c) 2022 MIT Laboratory for Computational Physiology
+
+The MIT Laboratory for Computational Physiology (MIT-LCP) wishes to make data available for research and educational purposes to qualified requestors, but only if the data are used and protected in accordance with the terms and conditions stated in this License.
+
+It is hereby agreed between the data requestor, hereinafter referred to as the "LICENSEE", and MIT-LCP, that:
+
+    The LICENSEE will not attempt to identify any individual or institution referenced in PhysioNet restricted data.
+    The LICENSEE will exercise all reasonable and prudent care to avoid disclosure of the identity of any individual or institution referenced in PhysioNet restricted data in any publication or other communication.
+    The LICENSEE will not share access to PhysioNet restricted data with anyone else.
+    The LICENSEE will exercise all reasonable and prudent care to maintain the physical and electronic security of PhysioNet restricted data.
+    If the LICENSEE finds information within PhysioNet restricted data that he or she believes might permit identification of any individual or institution, the LICENSEE will report the location of this information promptly by email to PHI-report@physionet.org, citing the location of the specific information in question.
+    The LICENSEE will use the data for the sole purpose of lawful use in scientific research and no other.
+    The LICENSEE will be responsible for ensuring that he or she maintains up to date certification in human research subject protection and HIPAA regulations.
+    The LICENSEE agrees to contribute code associated with publications arising from this data to a repository that is open to the research community.
+    This agreement may be terminated by either party at any time, but the LICENSEE's obligations with respect to PhysioNet data shall continue after termination.
+
+THE DATA ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DATA OR THE USE OR OTHER DEALINGS IN THE DATA.
+"""
+PhysioNetLicense1p5 = CustomLicense(
+    name="PhysioNet Credentialed Health Data License",
+    version="1.5",
+    link="https://physionet.org/content/mimiciv/view-license/0.4/",
+    # NOTE: just in case the link will break
+    text=_PHYSIONET_LICENSE_1p5_TEXT,
+)
+
+
+UMLSLicense = CustomLicense(
+    name="UMLS - Metathesaurus License Agreement",
+    link="https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html",
+)
+
+_NCBI_LICENSE_TEXT = """
+===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+*
+===========================================================================
+"""
+NCBILicense = CustomLicense(
+    name="National Center fr Biotechnology Information PUBLIC DOMAIN NOTICE",
+    link="https://github.com/openbiocorpora/genetag/blob/master/LICENSE",
+    # NOTE: just in case link will break
+    text=_NCBI_LICENSE_TEXT,
+)
+
+PublicDomainMark_1p0 = CustomLicense(
+    name="Public Domain Mark 1.0",
+    text="""This work has been identified as being free of known restrictions under copyright law,
+    including all related and neighboring rights.
+    """,
+    link="https://creativecommons.org/publicdomain/mark/1.0/",
+)
+
+
+def _get_variable_name(k: str) -> str:
+
+    return k.replace("-", "_").upper().replace(".", "p").replace("+", "plus")
+
+
+def load_json_licenses() -> Dict[str, str]:
+    """
+    Load all licenses from JSON file.
+    Amend names to be valid variable names
+    """
+
+    # shamelessly compied from:
+    # https://github.com/huggingface/datasets/blob/master/src/datasets/utils/metadata.py
+    licenses = {_get_variable_name(k): v for k, v in LICENSES_DATA.items()}
+
+    licenses["ZERO_BSD"] = licenses.pop("0BSD")
+
+    return licenses
+
+
+def load_licenses() -> Dict[str, License]:
+    """
+    Load `_LICENSES` dict:
+        - key (str) : license name
+        - value (License) : instance of license class
+    """
+
+    json_licenses = load_json_licenses()
+
+    json_licenses.update({"DUA": "Data User Agreement"})
+
+    licenses_kwargs = {k: {"name": v} for k, v in json_licenses.items()}
+
+    licenses = {k: License(**kwargs) for k, kwargs in licenses_kwargs.items()}
+
+    custom_licenses = {
+        "PUBLIC_DOMAIN_MARK_1p0": PublicDomainMark_1p0,
+        "GENIA_PROJECT_LICENSE": GeniaProjectLicense,
+        "NLM_LICENSE": NLMLicense,
+        "NCBI_LICENSE": NCBILicense,
+        "UMLS_LICENSE": UMLSLicense,
+        "PHYSIONET_LICENSE_1p5": PhysioNetLicense1p5,
+    }
+
+    licenses.update(custom_licenses)
+    for k, v in licenses.items():
+        v.short_name = k
+
+    return licenses
+
+
+_LICENSES = load_licenses()
+Licenses = SimpleNamespace(**_LICENSES)

licenses.json → licenses_data.py

@@ -1,4 +1,4 @@
-{
+LICENSES_DATA = {
     "other": "Other license",
     "unknown": "License information unavailable",
     "0bsd": "BSD Zero Clause License",
@@ -47,12 +47,12 @@
     "blueoak-1.0.0": "Blue Oak Model License 1.0.0",
     "borceux": "Borceux license",
     "bsd-1-clause": "BSD 1-Clause License",
-    "bsd-2-clause": "BSD 2-Clause \"Simplified\" License",
+    "bsd-2-clause": 'BSD 2-Clause "Simplified" License',
     "bsd-2-clause-freebsd": "BSD 2-Clause FreeBSD License",
     "bsd-2-clause-netbsd": "BSD 2-Clause NetBSD License",
     "bsd-2-clause-patent": "BSD-2-Clause Plus Patent License",
     "bsd-2-clause-views": "BSD 2-Clause with views sentence",
-    "bsd-3-clause": "BSD 3-Clause \"New\" or \"Revised\" License",
+    "bsd-3-clause": 'BSD 3-Clause "New" or "Revised" License',
     "bsd-3-clause-attribution": "BSD with attribution",
     "bsd-3-clause-clear": "BSD 3-Clause Clear License",
     "bsd-3-clause-lbnl": "Lawrence Berkeley National Labs BSD variant license",
@@ -60,7 +60,7 @@
     "bsd-3-clause-no-nuclear-license-2014": "BSD 3-Clause No Nuclear License 2014",
     "bsd-3-clause-no-nuclear-warranty": "BSD 3-Clause No Nuclear Warranty",
     "bsd-3-clause-open-mpi": "BSD 3-Clause Open MPI variant",
-    "bsd-4-clause": "BSD 4-Clause \"Original\" or \"Old\" License",
+    "bsd-4-clause": 'BSD 4-Clause "Original" or "Old" License',
     "bsd-4-clause-uc": "BSD-4-Clause (University of California-Specific)",
     "bsd-protection": "BSD Protection License",
     "bsd-source-code": "BSD Source Code Attribution",
@@ -448,5 +448,5 @@
     "zlib-acknowledgement": "zlib/libpng License with Acknowledgement",
     "zpl-1.1": "Zope Public License 1.1",
     "zpl-2.0": "Zope Public License 2.0",
-    "zpl-2.1": "Zope Public License 2.1"
+    "zpl-2.1": "Zope Public License 2.1",
 }