make wording uniform

Author: mierzs

organization-organization/ror-organigram.ipynb

@@ -1,19 +1,28 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {
     "id": "0-62NAVa8DL0"
    },
    "source": [
-    "### Query ROR for an organization and the hierarchy of sub-organizations below it\n",
+    "### Query ROR for an organization and all its suborganizations\n",
     "\n",
-    "This notebook queries the [ROR API](https://ror.readme.io/) to construct a hierarchy of sub-organizations starting at a given organization. It takes a ROR URL or ID which is used to retrieve the organizations specified in the metadata field \"`relationships`\" with `\"type\"=Child` recursively to build a tree structure. The tree represents the hierarchy of sub-organizations and will be outputted.\n"
+    "This notebook queries the [ROR API](https://ror.readme.io/) for an organization and all its suborganizations. \n",
+    "It takes a ROR URL or ROR ID as input which is used as a starting point for recursively querying the ROR API for an organization's suborganizations specified in the metadata field \"`relationships`\" having the `\"type\"=Child`. \n",
+    "The hierarchy is represented as a tree and will be outputted.\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "id": "VaYUrh5n2iq9",
     "scrolled": true
@@ -31,7 +40,7 @@
     "id": "YmmrIwjv3QqG"
    },
    "source": [
-    "The input value for all following queries is a ROR URL or ID, e.g. '`https://ror.org/03vek6s52`' or '`03vek6s52`'."
+    "The input for this notebook is a ROR URL or ROR ID, e.g. '`https://ror.org/03vek6s52`' or '`03vek6s52`'."
    ]
   },
   {
@@ -81,7 +90,8 @@
      },
      "user_tz": -60
     },
-    "id": "YpwZ3mrC3dHO"
+    "id": "YpwZ3mrC3dHO",
+    "scrolled": true
    },
    "outputs": [],
    "source": [
@@ -101,8 +111,8 @@
     "#---- example execution\n",
     "# uncomment following lines to see the metadata for specified example_ror\n",
     "#import pprint\n",
-    "#organization = query_ror_api(example_ror)\n",
-    "#pprint.pprint(organization)"
+    "#organization_data = query_ror_api(example_ror)\n",
+    "#pprint.pprint(organization_data)"
    ]
   },
   {
@@ -111,7 +121,7 @@
     "id": "T25jtRBf3c1T"
    },
    "source": [
-    "But in this notebook we use it as a starting point to recursively query the ROR API using the relationship type \"`Child`\" to construct the organizational hierarchy below it."
+    "but in this notebook we use it as a starting point to recursively query the ROR API using the relationship type \"`Child`\" to construct the organizational hierarchy below it."
    ]
   },
   {
@@ -133,7 +143,10 @@
      "user_tz": -60
     },
     "id": "4jh1liI56A4x",
-    "outputId": "ea1cbf18-6c90-4aa3-bfcb-10addcaa9e8f"
+    "outputId": "ea1cbf18-6c90-4aa3-bfcb-10addcaa9e8f",
+    "pycharm": {
+     "is_executing": true
+    }
    },
    "outputs": [
     {

organization-people/freya_get_people_by_organization.ipynb

@@ -6,14 +6,14 @@
     "id": "etxiXTW668ZD"
    },
    "source": [
-    "### Query the FREYA PID Graph for all people affiliated with an organization\n",
+    "### Query the FREYA PID Graph for people affiliated with an organization\n",
     "\n",
-    "This notebook queries the [FREYA PID Graph](https://blog.datacite.org/powering-the-pid-graph/) via [Datacite's GraphQL API](https://api.datacite.org/graphql) to retrieve all people affiliated with an organization. It takes a ROR URL as input which is used to retrieve the according Grid and Ringgold ID of the organization and query the ORCID API with it [for affiliated people](https://info.orcid.org/faq/how-do-i-find-orcid-record-holders-at-my-institution/). From the resulting list of people we output the ORCID iDs."
+    "This notebook queries the [FREYA PID Graph](https://blog.datacite.org/powering-the-pid-graph/) via [Datacite's GraphQL API](https://api.datacite.org/graphql) to retrieve people affiliated with an organization. It takes a ROR URL as input which is used internally to retrieve the Grid ID from the ROR API and Ringgold ID from Wikidata and use these identifiers to [find ORCID record holders at the institution](https://info.orcid.org/faq/how-do-i-find-orcid-record-holders-at-my-institution/). From the resulting list of people we output the ORCID iDs."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "id": "8Mk7-aYc7x3A",
     "scrolled": true
@@ -31,7 +31,7 @@
     "id": "J31_ejB6bWqd"
    },
    "source": [
-    "The input for the query is a ROR URL, e.g. '`https://ror.org/021k10z87`'"
+    "The input for this notebook is a ROR URL, e.g. '`https://ror.org/021k10z87`'"
    ]
   },
   {
@@ -63,7 +63,8 @@
     "id": "ba_A3Anpbl4P"
    },
    "source": [
-    "We use it to query Datacite's GraphQL API for the organization's metadata and all people connected to it. Since the API uses pagination, we need to loop through all pages to get the complete result set.\n"
+    "We use it to query Datacite's GraphQL API for the organization's metadata and all people connected to it.\n",
+    "Since the API uses pagination, we need to loop through all pages to get the complete result set.\n"
    ]
   },
   {
@@ -176,20 +177,21 @@
      "text": [
       "0000-0002-3783-6130, Irene Weipert-Fenner\n",
       "0000-0002-5452-0488, Hans-Joachim Spanger\n",
-      "0000-0001-6746-1248, Anton Peez\n",
+      "0000-0002-4621-9687, Simone Schnabel\n",
       "0000-0001-6731-5304, Julia Eckert\n",
+      "0000-0001-6746-1248, Anton Peez\n",
       "0000-0003-1575-9688, Hendrik Simon\n",
       "0000-0002-1712-2624, Julian Junk\n",
       "0000-0003-0035-5840, Raphael Oidtmann\n",
       "0000-0002-5925-043X, Ariadne Natal\n",
       "0000-0002-7012-6739, Peter Kreuzer\n",
       "0000-0001-7843-4480, Dirk Peters\n",
-      "0000-0003-0039-9827, Eldad Ben Aharon\n",
       "0000-0001-6823-6819, Janna Lisa Chalmovsky\n",
       "0000-0003-1940-8877, Mikhail Polianskii\n",
       "0000-0001-7302-444X, Katja Freistein\n",
-      "0000-0001-7286-3575, Paul Chambers\n",
       "0000-0002-8739-2486, Elvira Rosert\n",
+      "0000-0001-7286-3575, Paul Chambers\n",
+      "0000-0003-0039-9827, Eldad Ben Aharon\n",
       "0000-0002-4259-6071, Felix S. Bethke\n"
      ]
     }

organization-people/openalex_get_people_by_organization.ipynb

@@ -7,14 +7,14 @@
     "id": "ac7bedaf-05fb-4eb0-9bf5-e4d1d68a08c3"
    },
    "source": [
-    "### Query OpenAlex for all people affiliated with an organization\n",
-    "This script queries the [OpenAlex API](https://docs.openalex.org/api) via its '`/authors`' endpoint for all authors affiliated with an organization.\n",
-    "It takes a ROR URL as input which is used to retrieve all authors that specified the ROR ID in their metadata field '`last_known_institution.ror`'. From the resulting list of people we output their respective ORCID iDs."
+    "### Query OpenAlex for people affiliated with an organization\n",
+    "This notebook queries the [OpenAlex API](https://docs.openalex.org/api) via its '`/authors`' endpoint for all authors affiliated with an organization.\n",
+    "It takes a ROR URL as input which is used to retrieve authors with the specified ROR URL in their metadata field '`last_known_institution.ror`'. From the resulting list of people we output the ORCID iDs."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "IUqshUWKwSk2",
    "metadata": {
     "executionInfo": {
@@ -43,7 +43,7 @@
     "id": "nSJjdkxGdWll"
    },
    "source": [
-    "The input for the query is a ROR URL, e.g. '`https://ror.org/021k10z87`'"
+    "The input for the notebook is a ROR URL, e.g. '`https://ror.org/021k10z87`'"
    ]
   },
   {
@@ -77,7 +77,7 @@
     "id": "MiXVDKXid9tq"
    },
    "source": [
-    "We use it to query the OpenAlex API for authors that specified the organization's ROR ID in the field '`last_known_institution.ror`'.  Since the OpenAlex API uses [pagination](https://docs.openalex.org/api/get-lists-of-entities#pagination), we need to loop through all pages to get the complete result set."
+    "We use it to query the OpenAlex API endpoint for `'authors'` with the specified ROR URL in their metadata field '`last_known_institution.ror`'.  Since the API uses [pagination](https://docs.openalex.org/api/get-lists-of-entities#pagination), we need to loop through all pages to get the complete result set."
    ]
   },
   {
@@ -141,7 +141,9 @@
     "id": "CwRzvAQweuoW"
    },
    "source": [
-    "From the resulting list of people we extract and print out each ORCID and name."
+    "From the resulting list of people we extract and print out each ORCID iD and name.\n",
+    "\n",
+    "*Note: people that do not have an ORCID within their `ids` metadata, will not be printed.*"
    ]
   },
   {
@@ -173,15 +175,15 @@
      "text": [
       "0000-0002-3824-5375, Nicole Deitelhoff\n",
       "0000-0002-7348-7206, Jonas Wolff\n",
-      "0000-0002-6891-770X, Francis O’Connor\n",
       "0000-0002-3536-8898, Felix Anderl\n",
       "0000-0002-4259-6071, Felix S. Bethke\n",
       "0000-0002-3136-0901, Thorsten Gromes\n",
       "0000-0001-9698-2616, Annika Elena Poppe\n",
       "0000-0002-3783-6130, Irene Weipert-Fenner\n",
       "0000-0002-4793-9010, Arvid Bell\n",
       "0000-0002-7012-6739, Peter Kreuzer\n",
-      "0000-0002-0143-5183, Christina Kohler\n"
+      "0000-0002-1185-8673, Daniel Mullis\n",
+      "0000-0001-6746-1248, Anton Peez\n"
      ]
     }
    ],

person-works/crossref_get_works_by_person.ipynb

@@ -6,14 +6,14 @@
     "id": "k6HfuEZe48LV"
    },
    "source": [
-    "### Query Crossref for all works authored by a person\n",
-    "This notebook queries the [Crossref API](http://api.crossref.org) via its `/works` endpoint for all works authored by a person. It takes an ORCID URL as input which is used to filter for all works where one of the authors' ORCID field matches the given ORCID URL.\n",
-    "From the resulting list of works we output their respective DOIs."
+    "### Query Crossref for works authored by a person\n",
+    "This notebook queries the [Crossref API](http://api.crossref.org) via its `'/works'` endpoint for works authored by a person. It takes an ORCID URL or ORCID iD as input which is used to filter for all works where one of the authors' `orcid` field matches the given ORCID iD.\n",
+    "From the resulting list of works we output all DOIs."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "id": "aV_HkXxJ4pVB",
     "scrolled": true
@@ -31,7 +31,7 @@
     "id": "4z7u62G76IBh"
    },
    "source": [
-    "The input for the query is an ORCID URL or an ORCID iD, e.g. '`https://orcid.org/0000-0003-2499-7741`' or '`0000-0003-2499-7741`'"
+    "The input for this notebook is an ORCID URL or ORCID iD, e.g. '`https://orcid.org/0000-0003-2499-7741`' or '`0000-0003-2499-7741`'"
    ]
   },
   {
@@ -63,7 +63,7 @@
     "id": "uYK5apGy6i4f"
    },
    "source": [
-    "We use it to query the Crossref API via its '`/works`' endpoint and set a filter for the given ORCID iD."
+    "We use it to query the Crossref API via its '`/works`' endpoint and set a filter for the `orcid` field to match the given ORCID iD."
    ]
   },
   {

person-works/freya_get_works_by_person.ipynb

@@ -8,12 +8,12 @@
    "source": [
     "### Query the FREYA PID Graph for works authored by a person\n",
     "\n",
-    "This notebook queries the [FREYA PID Graph](https://blog.datacite.org/powering-the-pid-graph/) via [Datacite's GraphQL API](https://api.datacite.org/graphql) to retrieve all works created by a person. It takes an ORCID URL as input which is used to filter for all works registered at Datacite and some registered at Crossref where '`creator.nameIdentifier`' matches the given ORCID URL. From the resulting list of works we output their respective DOIs."
+    "This notebook queries the [FREYA PID Graph](https://blog.datacite.org/powering-the-pid-graph/) via [Datacite's GraphQL API](https://api.datacite.org/graphql) to retrieve works created by a person. It takes an ORCID URL as input which is used to filter for all works registered at Datacite and some registered at Crossref where '`creator.nameIdentifier`' matches the given ORCID URL. From the resulting list of works we output all DOIs."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "id": "CCRX2-tC_ijb",
     "scrolled": true
@@ -31,7 +31,7 @@
     "id": "9J5pNonyPXzZ"
    },
    "source": [
-    "The input for the query is an ORCID URL, e.g. '`https://orcid.org/0000-0003-2499-7741`'."
+    "The input for this notebook is an ORCID URL, e.g. '`https://orcid.org/0000-0003-2499-7741`'."
    ]
   },
   {
@@ -160,8 +160,8 @@
     "* remove the ones that are older versions of another work, which is the case if the metadata field for '`versions.nodes.doi`' contains a DOI for the successing work,\n",
     "* extract and print out the title and DOI of each work.\n",
     "\n",
-    "Note: \n",
-    "While we are able to filter some versions of a work if they are linked via the metadata field '`versions.nodes.doi`', others would need advanced filters (for example based on name similarity) which is out of scope for our project."
+    "*Note: \n",
+    "While we are able to filter some versions of a work if they are linked via the metadata field '`versions.nodes.doi`', others would need advanced filters (for example based on name similarity) which is out of scope for our project.*"
    ]
   },
   {

person-works/openalex_get_works_by_person.ipynb

@@ -7,14 +7,14 @@
     "id": "ac7bedaf-05fb-4eb0-9bf5-e4d1d68a08c3"
    },
    "source": [
-    "### Query OpenAlex for all works authored by a person\n",
-    "This notebook queries the [OpenAlex API](https://docs.openalex.org/api) via its `/works` endpoint for all works authored by a person. It takes an ORCID URL as input which is used to filter for all works where '`authorships.author.orcid`' matches the given ORCID URL.\n",
-    "From the resulting list of works we output their respective DOIs."
+    "### Query OpenAlex for works authored by a person\n",
+    "This notebook queries the [OpenAlex API](https://docs.openalex.org/api) via its `/works` endpoint for works authored by a person. It takes an ORCID URL as input which is used to filter for works where '`authorships.author.orcid`' matches the given ORCID URL.\n",
+    "From the resulting list of works we output all DOIs."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "W8sB1ZF6aKG2",
    "metadata": {
     "executionInfo": {
@@ -79,7 +79,7 @@
    },
    "source": [
     "We use it to query the OpenAlex API for works that specified the ORCID URL within their metadata in the field '`authorships.author.orcid`'.\n",
-    " Since the OpenAlex API uses [pagination](https://docs.openalex.org/api/get-lists-of-entities#pagination), we need to loop through all pages to get the complete result set."
+    " Since the API uses [pagination](https://docs.openalex.org/api/get-lists-of-entities#pagination), we need to loop through all pages to get the complete result set."
    ]
   },
   {
@@ -143,7 +143,9 @@
     "id": "kHRO_LiJr-u_"
    },
    "source": [
-    "From the resulting list of works we extract and print out title and DOI."
+    "From the resulting list of works we extract and print out title and DOI. \n",
+    "\n",
+    "*Note: works that do not have a DOI assigned, will not be printed.*"
    ]
   },
   {
@@ -186,9 +188,9 @@
       "10.5281/zenodo.1464108, VIVO - eine Einführung\n",
       "10.11588/ip.2018.1.46819, Anforderungen an Forschungsinformationssysteme in Deutschland durch Forschende und Forschungsadministration – Zusammenfassung zweier Studien\n",
       "10.5281/zenodo.1287885, Supporting a VIVO Regional Community\n",
-      "10.15488/3951, Reporting mit VIVO und Kibana\n",
-      "10.15488/3952, Forschungsevaluation und Visualisierung von Zitationsnetzwerken\n",
       "10.15488/4087, Referenzimplementierung für offene szientometrische Indikatoren (ROSI)\n",
+      "10.15488/3952, Forschungsevaluation und Visualisierung von Zitationsnetzwerken\n",
+      "10.15488/3951, Reporting mit VIVO und Kibana\n",
       "10.11588/ip.2017.2.41926, Tagungsbericht VIVO-Workshop 2017 - “Forschungsinformationen in der Praxis”\n",
       "10.11588/ip.2016.2.32678, Third-Party-Elemente in deutschen Bibliothekswebseiten\n",
       "10.11588/ip.2016.1.31963, Editorial – Rückblick und Call for Call for Papers\n",
@@ -204,8 +206,8 @@
       "10.25968/opus-303, Lernen 2.0 : Bericht aus der Praxis\n",
       "10.17877/de290r-8755, Web 2.0 in Bibliotheken - Bibliotheken im Web 2.0\n",
       "10.18452/8872, Libworld. Biblioblogs global\n",
-      "10.1515/bd.2006.40.4.466, Informationsvermittlung: Personalisiertes Lernen in der Bibliothek: das Düsseldorfer Online-Tutorial (DOT) Informationskompetenz\n",
-      "10.1080/00048623.2006.10755322, Teaching Information Literacy with the Lerninformationssystem\n"
+      "10.1080/00048623.2006.10755322, Teaching Information Literacy with the Lerninformationssystem\n",
+      "10.1515/bd.2006.40.4.466, Informationsvermittlung: Personalisiertes Lernen in der Bibliothek: das Düsseldorfer Online-Tutorial (DOT) Informationskompetenz\n"
      ]
     }
    ],

person-works/orcid_get_works_by_person.ipynb

@@ -8,12 +8,12 @@
    "source": [
     "### Query ORCID for works authored by a person\n",
     "\n",
-    "This notebook queries the [ORCID API](https://pub.orcid.org/v3.0/) to retrieve all works listed in a person's ORCID profile. It takes an ORCID URL or iD as input to retrieve the ORCID profile of a person and the works listed on it. From the list of works we output their respective DOIs."
+    "This notebook queries the [ORCID API](https://pub.orcid.org/v3.0/) to retrieve works listed in a person's ORCID record. It takes an ORCID URL or iD as input to retrieve the ORCID record of a person and the works listed on it. From the resulting list of works we output all DOIs."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "id": "8OqUUX037qB4",
     "scrolled": true
@@ -31,7 +31,7 @@
     "id": "G3oSBrNo8rb-"
    },
    "source": [
-    "The input for the query is an ORCID URL or ORCID iD, e.g. '`https://orcid.org/0000-0003-2499-7741`' or '`0000-0003-2499-7741`'."
+    "The input for this notebook is an ORCID URL or iD, e.g. '`https://orcid.org/0000-0003-2499-7741`' or '`0000-0003-2499-7741`'."
    ]
   },
   {
@@ -63,7 +63,7 @@
     "id": "sD-zpjgT9_rn"
    },
    "source": [
-    "We use it to query ORCID for the person's metadata and all works connected to them."
+    "We use it to query ORCID's Public API for the person's metadata and all works connected to them."
    ]
   },
   {
@@ -103,7 +103,7 @@
     "orcid_record=query_orcid_for_record(orcid_id)\n",
     "# uncomment next lines to see complete metadata for given ORCID\n",
     "#import pprint\n",
-    "#pprint.pprint(orcid_data)"
+    "#pprint.pprint(orcid_record)"
    ]
   },
   {
@@ -112,7 +112,9 @@
     "id": "gZ43Wyp7_qVu"
    },
    "source": [
-    "From the complete ORCID metadata we extract the works section and print out title and DOI of each first work-summary (the first item in a personal information section has the highest [display index](https://info.orcid.org/documentation/integration-guide/orcid-record/#Display_index))."
+    "From the complete ORCID metadata we extract the works section and print out title and DOI of each first `work-summary` (the first item in a personal information section has the highest [display index](https://info.orcid.org/documentation/integration-guide/orcid-record/#Display_index)).\n",
+    "\n",
+    "*Note: works that do not have a DOI assigned, will not be printed.*"
    ]
   },
   {