Add Zenodo button and CITATION.cff (#242)

Closes #241. Also:
* Replaces `TranslatorSRI` with `NCATSTranslator` in some places.
* Adds `/.idea/` to .gitignore.
* Adds Zenodo and arXiv buttons to the README.

Author: gaurav

.gitignore

@@ -1,4 +1,7 @@
 venv/
 .vscode/
 __pycache__/
-data/
+data/
+
+# IntelliJ files
+/.idea/

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

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.

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.<p/>
     Multiple results may be returned representing possible conceptual matches, but all of the identifiers
     have been correctly normalized using the
-    <a href="https://github.com/TranslatorSRI/NodeNormalization">Node Normalization</a> service.<p/>You can read more
+    <a href="https://github.com/NCATSTranslator/NodeNormalization">Node Normalization</a> service.<p/>You can read more
     about this API on the <a href="https://github.com/NCATSTranslator/NameResolution">NameResolution GitHub repository</a>.<p/>
     Note that the returned by this service have been conflated using both GeneProtein and DrugChemical conflation;
     you can read more about this at the <a href="https://github.com/NCATSTranslator/Babel/blob/master/docs/Conflation.md">Conflation documentation</a>.'

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))
 

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

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", "--" ]

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: .