Merge pull request #179 from UA-Libraries-Research-Data-Services/fix-citation-download

Fix citation download

Author: dachambers

rmarkdown/pubchem.Rmd

@@ -41,7 +41,7 @@ Please see the following resources for more information on API usage:
 
 **Attribution:** This tutorial was adapted from supporting information in:
 
-**Scalfani, V. F.**; Ralph, S. C. Alshaikh, A. A.; Bara, J. E. Programmatic Compilation of Chemical Data and Literature From PubChem Using Matlab. *Chemical Engineering Education*, **2020**, *54*, 230. https://doi.org/10.18260/2-1-370.660-115508 and https://github.com/vfscalfani/MATLAB-cheminformatics
+**Scalfani, V. F.**; Ralph, S. C. Alshaikh, A. A.; Bara, J. E. Programmatic Compilation of Chemical Data and Literature From PubChem Using Matlab. *Chemical Engineering Education*, **2020**, *54*, 230. https://doi.org/10.18260/2-1-370.660-115508 and https://github.com/UA-Libraries-Research-Data-Services/MATLAB-cheminformatics
 
 ## Setup
 

src/_static/CITATION.bib

@@ -0,0 +1,14 @@
+@article{scalfani_creating_2023,
+        title = {Creating a {Scholarly} {API} {Cookbook}: {Supporting} {Library} {Users} with {Programmatic} {Access} to {Information}},
+        issn = {1092-1206},
+        shorttitle = {Creating a {Scholarly} {API} {Cookbook}},
+        url = {https://journals.library.ualberta.ca/istl/index.php/istl/article/view/2766},
+        doi = {10.29173/istl2766},
+        abstract = {Scholarly web-based application programming interfaces (APIs) allow users to interact with information and data programmatically. Interacting with information programmatically allows users to create advanced information query workflows and quickly access machine-readable data for downstream computations. With the growing availability of scholarly APIs from open and commercial library databases, supporting access to information via an API has become a key support area for research data services in libraries. This article describes our efforts with supporting API access through the development of an online Scholarly API Cookbook. The Cookbook contains code recipes (i.e., tutorials) for getting started with 10 different scholarly APIs, including for example, Scopus, World Bank, and PubMed. API tutorials are available in Python, Bash, Matlab, and Mathematica. A tutorial for interacting with library catalog data programmatically via Z39.50 is also included, as traditional library catalog metadata is rarely available via an API. In addition to describing the Scholarly API Cookbook content, we discuss our experiences building a student research data services programming team, challenges we encountered, and ideas to improve the Cookbook. The University of Alabama Libraries Scholarly API Cookbook is freely available and hosted on GitHub. All code within the API Cookbook is licensed with the permissive MIT license, and as a result, users are free to reuse and adapt the code in their teaching and research.},
+        number = {104},
+        urldate = {2023-10-13},
+        journal = {Issues in Science and Technology Librarianship},
+        author = {Scalfani, Vincent F. and Walker, Kevin W. and Simpson, Lance and Fernandez, Avery M. and Patel, Vishank D. and Ramig, Anastasia and Gomes, Cyrus and Moen, Michael T. and Nguyen, Adam M.},
+        month = oct,
+        year = {2023},
+}

src/about/cite.rst

@@ -1,7 +1,9 @@
 Citing the Cookbook
 %%%%%%%%%%%%%%%%%%%%
 
-If you reuse the code, attribution would be appreciated. Please link to the Cookbook and cite our manuscript:
+If you reuse the code, attribution would be appreciated. Please link to the Cookbook tutorial 
+page and attribute the authors and UA Libraries for the tutorial (see each tutorial page for authors). 
+If you use or are referring to the Cookbook in scholarship, please also consider citing our manuscript:
 
 Link to Cookbook: `<https://ua-libraries-research-data-services.github.io/UALIB_ScholarlyAPI_Cookbook>`_
 
@@ -28,7 +30,7 @@ Citation: Scalfani, V. F.; Walker, K. W.; Simpson, L.; Fernandez, A. M.; Patel,
 
     <div class="rmd-btn-wrapper">
       <a class="rmd-btn"
-         href="../../CITATION.bib"
+         href="../_static/CITATION.bib"
          download>
         Download CITATION.bib
       </a>

src/overview/college-scorecard.rst

@@ -10,7 +10,7 @@ See the Department of Education's website for more information on how the data o
 
 .. rubric:: References
 
-.. [#cs1] `<https://collegescorecard.ed.gov/data/api-documentation#api-access-and-authentication>`_
+.. [#cs1] `<https://collegescorecard.ed.gov/data/api-documentation>`_
 
 .. [#cs2] `<https://collegescorecard.ed.gov/data>`_
 

src/overview/openalex.rst

@@ -12,7 +12,7 @@ See the OpenAlex API documentation [#oa2]_ for more information on accessing the
 
 .. [#oa1] `<https://ourresearch.org/>`_
 
-.. [#oa2] `<https://docs.openalex.org/>`_
+.. [#oa2] `<https://developers.openalex.org/>`_
 
 .. [#oa3] `<https://creativecommons.org/publicdomain/zero/1.0/>`_
 

src/overview/pubchem-periodic-table.rst

@@ -14,7 +14,7 @@ See the PubChem Periodic Table [#ppt1]_ and PubChem APIs documentation [#ppt2]_
 
 .. [#ppt1] `<https://pubchem.ncbi.nlm.nih.gov/periodic-table/>`_
 
-.. [#ppt2] `<https://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access>`_
+.. [#ppt2] `<https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access>`_
 
 .. [#ppt3] `<https://www.ncbi.nlm.nih.gov/home/about/policies/>`_
 

src/overview/pubchem.rst

@@ -8,5 +8,5 @@ PubChem APIs allow programmatic access to search and retrieve small molecule and
 
 .. rubric:: References
 
-.. [#pubchem1] `<https://pubchemdocs.ncbi.nlm.nih.gov/about>`_
+.. [#pubchem1] `<https://pubchem.ncbi.nlm.nih.gov/docs/about>`_
  

src/overview/wos.rst

@@ -26,4 +26,4 @@ Please see the WOS API release notes [#wos4]_ to stay up-to-date on the APIs. Se
 
 .. [#wos5] `<https://clarivate.com/wp-content/uploads/dlm_uploads/2019/08/End-User-Terms.pdf>`_
 
-.. [#wos6] `<https://clarivate.com/wp-content/uploads/dlm_uploads/2023/12/Product-Terms-v3.7-Web-of-Science-APIs.pdf>`_
+.. [#wos6] `<https://clarivate.com/legal-center/terms-of-business/product-service-terms/>`_

src/python/crossref.ipynb

@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "id": "4c9acd0e",
    "metadata": {},
    "source": [
     "# Crossref API in Python\n",

src/python/openalex.ipynb

@@ -66,7 +66,7 @@
     "\n",
     "An API key is required to access the OpenAlex API. Please see the <a href=\"https://developers.openalex.org/guides/authentication\" target=\"_blank\">Authentication & Pricing page</a> for instructions on how to obtain one.\n",
     "\n",
-    "We keep our email in a `.env` file and use the `dotenv` library to access it. If you would like to use this method, create a `.env` file and add the following line to it:\n",
+    "We keep our API key in a `.env` file and use the `dotenv` library to access it. If you would like to use this method, create a `.env` file and add the following line to it:\n",
     "\n",
     "```text\n",
     "OPENALEX_API_KEY=\"YOUR-API-KEY-HERE\"\n",