diff --git a/.gitignore b/.gitignore index 29d4f1d5..4b8ab74b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,7 @@ venv/ .vscode/ __pycache__/ -data/ \ No newline at end of file +data/ + +# IntelliJ files +/.idea/ diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..f22984f3 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,34 @@ +cff-version: 1.2.0 +type: software +authors: + - family-names: "Bizon" + given-names: "Chris" + email: bizon@renci.org + affiliation: Renaissance Computing Institute, University of North Carolina + orcid: "https://orcid.org/0000-0002-9491-7674" + - family-names: "Vaidya" + given-names: "Gaurav" + email: gaurav@renci.org + affiliation: Renaissance Computing Institute, University of North Carolina + orcid: "https://orcid.org/0000-0003-0587-0454" + - family-names: "Wang" + given-names: "Patrick" + affiliation: Duke University + orcid: "https://orcid.org/0000-0002-6693-6106" + - family-names: "Owen" + given-names: "Phillips" + affiliation: Renaissance Computing Institute, University of North Carolina + orcid: "https://orcid.org/0000-0002-5146-8434" + - family-names: "Kebede" + given-names: "Yaphet" + affiliation: Renaissance Computing Institute, University of North Carolina + orcid: "https://orcid.org/0000-0002-50460246" +title: "Name Resolver" +url: "https://github.com/NCATSTranslator/NameResolution" +repository-code: "https://github.com/NCATSTranslator/NameResolution" +abstract: >- + Name Resolver (Name Lookup or NameRes) takes lexical strings and attempts to map them to identifiers (CURIEs) from a vocabulary or ontology. +license: MIT +identifiers: + - type: doi + value: 10.5281/zenodo.18488923 diff --git a/README.md b/README.md index 12411a2a..79c60fe0 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # Name Resolver +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18488923.svg)](https://doi.org/10.5281/zenodo.18488923) [![arXiv](https://img.shields.io/badge/arXiv-2601.10008-b31b1b.svg)](https://arxiv.org/abs/2601.10008) + Name Resolver (Name Lookup or NameRes) takes lexical strings and attempts to map them to identifiers (CURIEs) from a vocabulary or ontology. An optional autocomplete mode (which assumes the query is incomplete) is available, along with many other options. Given a preferred CURIE, the known synonyms of that CURIE can also be retrieved. Multiple results may be returned representing possible conceptual matches, but all of the identifiers have been correctly normalized using the [Node Normalization](https://github.com/NCATSTranslator/NodeNormalization) service. diff --git a/api/resources/openapi.yml b/api/resources/openapi.yml index 588a2212..a9647e0b 100644 --- a/api/resources/openapi.yml +++ b/api/resources/openapi.yml @@ -11,7 +11,7 @@ info: along with many other options. Given a preferred CURIE, the known synonyms of that CURIE can also be retrieved.

Multiple results may be returned representing possible conceptual matches, but all of the identifiers have been correctly normalized using the - Node Normalization service.

You can read more + Node Normalization service.

You can read more about this API on the NameResolution GitHub repository.

Note that the returned by this service have been conflated using both GeneProtein and DrugChemical conflation; you can read more about this at the Conflation documentation.' diff --git a/api/server.py b/api/server.py index 58518996..955193fc 100755 --- a/api/server.py +++ b/api/server.py @@ -391,7 +391,7 @@ async def lookup(string: str, # - https://pypi.org/project/charset-normalizer/ # - https://www.crummy.com/software/BeautifulSoup/bs4/doc/#unicode-dammit # But the only issue we've actually run into so far has been the Windows smart - # quote (https://github.com/TranslatorSRI/NameResolution/issues/176), so for now + # quote (https://github.com/NCATSTranslator/NameResolution/issues/176), so for now # let's detect and replace just those characters. string_lc = re.sub(r"[“”]", '"', re.sub(r"[‘’]", "'", string_lc)) diff --git a/data-loading/Dockerfile b/data-loading/Dockerfile index bddef400..331b9fcc 100644 --- a/data-loading/Dockerfile +++ b/data-loading/Dockerfile @@ -2,7 +2,7 @@ # # A NameResolution worker is a SOLR instance that downloads its source file a SOLR database backup. # (see ../Dockerfile and [1] for details). This Dockerfile is intended to create a SOLR instance that can load the -# data from a set of Babel synonym files (see https://github.com/TranslatorSRI/Babel), thus creating the SOLR backup +# data from a set of Babel synonym files (see https://github.com/NCATSTranslator/Babel), thus creating the SOLR backup # which can be uploaded somewhere for the NameResolution workers. # # [1] https://github.com/helxplatform/translator-devops/blob/affcf34cf103230d25bdb859098d2a5ac81a49fb/helm/name-lookup/templates/scripts-config-map.yaml#L8-L105 diff --git a/data-loading/kubernetes/nameres-loading.k8s.yaml b/data-loading/kubernetes/nameres-loading.k8s.yaml index 525b9730..9460c284 100644 --- a/data-loading/kubernetes/nameres-loading.k8s.yaml +++ b/data-loading/kubernetes/nameres-loading.k8s.yaml @@ -1,4 +1,4 @@ -# Kubernetes file for Nameres-loading +# Kubernetes file for Nameres-loading apiVersion: v1 kind: Pod @@ -10,7 +10,7 @@ spec: restartPolicy: Never containers: - name: nameres-loading - image: ghcr.io/translatorsri/nameresolution-data-loading:latest + image: ghcr.io/ncatstranslator/nameresolution-data-loading:latest imagePullPolicy: Always # I just need something to run while I figure out how to make this work command: [ "/bin/bash", "-c", "--" ] diff --git a/docker-compose.yml b/docker-compose.yml index 78a38e74..3d4c7aa2 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -30,6 +30,6 @@ services: # This will use the latest version of NameRes -- if you'd prefer to build an image using the Dockerfile # in the current directory, remove the `:latest` tag and uncomment the `build:` section that follows it. - image: ghcr.io/translatorsri/nameresolution:latest + image: ghcr.io/ncatstranslator/nameresolution:latest # build: # context: .