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Rename dump to dataset

This commit is contained in:
Serafeim Chatzopoulos 2024-01-17 11:36:15 +02:00
parent c801abe833
commit 4b27dd22ae
9 changed files with 25 additions and 27 deletions
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docs/apis/specification-changelog.md
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| 2022-09-28T20:35:13.116653Z | updated URLs to the broker swagger UI |
| 2022-07-28T12:02:06.271154Z | Updated list of funders supported by the API for bulk access to projects: EC Horizon Europe also included |
| 2022-05-11T10:01:33.969973Z | New end point for researchProducts in selective access! FOS and SDG classifications available for publication requests |
| 2022-03-29T15:03:29.583536Z | Graph dumps: add new Scholix version 4 |
| 2022-03-29T15:03:29.583536Z | Graph dataset: add new Scholix version 4 |
| 2021-11-12T12:04:52.900385Z | originalId parameter added |
| 2021-10-18T15:31:18.446582Z | OAI-PMH publisher completely dismissed as announced in January 2021 |
| 2021-10-12T07:46:48.032978Z | orcid parameter added in selective access |
| 2021-04-08T10:28:02.371361Z | Authenticated requests to our APIs are now enabled. |
| 2021-02-26T16:28:15.364435Z | NEWS: new dump available with research products with project funding information |
| 2021-02-26T16:28:15.364435Z | NEWS: new dataset available with research products with project funding information |
| 2021-02-17T07:39:46.051129Z | WIP: broker API documentation |
| 2021-02-11T09:06:41.608115Z | Broker API documentation |
| 2021-02-10T10:17:39.504429Z | Authentication documentation added + broker card + broker dummy page |
| 2021-02-01T08:55:35.496938Z | OAI-PMH shutdown announced for the end of April 2021 |
| 2021-01-15T18:56:04.748404Z | Updated documentation on OpenAIRE Research Graph dumps |
| 2021-01-15T18:56:04.748404Z | Updated documentation on OpenAIRE Research Graph Datasets |
| 2021-01-15T16:57:08.569766Z | Announcing the shutdown of the OAI-PMH publisher |
| 2019-01-25T15:36:27.264313Z | Added new parameter country for research results |
| 2018-10-17T10:39:56.570815Z | Software and Other research products are available via HTTP API. Documentation has been updated. |

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docs/changelog.md
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@ -20,7 +20,7 @@ This section documents all notable changes for each graph version.
---
### v7.0.0
_Start Date: 2023-12-18 • Release Date: 2024-01-06 • Dump release: **yes**_
_Start Date: 2023-12-18 • Release Date: 2024-01-06 • Dataset release: **yes**_
#### Added
@ -38,7 +38,7 @@ This graph release also introduces new indicators to identify results published
- `result.publicly-funded (true, false)`: indicates whether or not the grants acknowledged by the publication come from public funds.
### v6.2.2
_Start Date: 2023-11-07 • Release Date: 2023-11-23 • Dump release: **no**_
_Start Date: 2023-11-07 • Release Date: 2023-11-23 • Dataset release: **no**_
#### Added
- Imported Opencitation's POCI dataset, containing citations among publications in PubMed
@ -55,7 +55,7 @@ _Start Date: 2023-11-07 • Release Date: 2023-11-23 • Dump release: **n
- Indicators regarding data source downloads and views taken by usage counts from September 2023
### v6.1.1
_Start Date: 2023-09-11 • Release Date: 2023-10-15 • Dump release: **no**_
_Start Date: 2023-09-11 • Release Date: 2023-10-15 • Dataset release: **no**_
#### Added
- Affiliation (result to organization) relations from Crossref
@ -71,7 +71,7 @@ _Start Date: 2023-09-11 • Release Date: 2023-10-15 • Dump release: **n
- OpenCitations relations from December 2022
### v6.0.0
_Start Date: 2023-07-26 • Release Date: 2023-08-16 • Dump release: **yes**_
_Start Date: 2023-07-26 • Release Date: 2023-08-16 • Dataset release: **yes**_
#### Changed
@ -87,7 +87,7 @@ _Start Date: 2023-07-26 • Release Date: 2023-08-16 • Dump release: **y
### v5.2.0
_Start Date: 2023-07-03 • Release Date: 2023-07-17 • Dump release: **no**_
_Start Date: 2023-07-03 • Release Date: 2023-07-17 • Dataset release: **no**_
#### Added
- Citations imported from Crossref & MAG
@ -106,7 +106,7 @@ _Start Date: 2023-07-03 • Release Date: 2023-07-17 • Dump release: **n
- Avoid duplicated organisation PIDs
### v5.1.3
_Start Date: 2023-05-22 • Release Date: 2023-06-12 • Dump release: **no**_
_Start Date: 2023-05-22 • Release Date: 2023-06-12 • Dataset release: **no**_
#### Added
- Datasource and project level usage counts
@ -121,7 +121,7 @@ _Start Date: 2023-05-22 • Release Date: 2023-06-12 • Dump release: **n
- Deduplication of the datasource
### v5.1.2
_Start Date: 2023-03-20 • Release Date: 2023-04-04 • Dump release: **no**_
_Start Date: 2023-03-20 • Release Date: 2023-04-04 • Dataset release: **no**_
#### Changed
@ -132,7 +132,7 @@ _Start Date: 2023-03-20 • Release Date: 2023-04-04 • Dump release: **n
- OpenCitations relations from January 2023
### v5.1.1
_Start Date: 2023-02-13 • Release Date: 2023-03-01 • Dump release: **no**_
_Start Date: 2023-02-13 • Release Date: 2023-03-01 • Dataset release: **no**_
#### Added
@ -151,7 +151,7 @@ _Start Date: 2023-02-13 • Release Date: 2023-03-01 • Dump release: **n
- OpenCitations relations from December 2022
### v5.1.0
_Start Date: 2023-01-16 • Release Date: 2023-01-30 • Dump release: **no**_
_Start Date: 2023-01-16 • Release Date: 2023-01-30 • Dataset release: **no**_
#### Added
@ -168,7 +168,7 @@ _Start Date: 2023-01-16 • Release Date: 2023-01-30 • Dump release: **n
### v5.0.0
_Start Date: 2022-12-19 • Release Date: 2022-12-28 • Dump release: **yes**_
_Start Date: 2022-12-19 • Release Date: 2022-12-28 • Dataset release: **yes**_
#### Added

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docs/data-model/relationships/relationship-types.md
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# Relationship types
The following table lists all the possible relation semantics found in the graph dump.
The following table lists all the possible relation semantics found in the Graph Dataset.
Note: the labels used to specify the semantic of the relationships are (for the large) inherited from the [DataCite metadata kernel](https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf), which provides a description for them.

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# Beginner's kit
<!-- :::caution
This version is not accompanied with public dump files, hence the files in this section are based on [v6.0.0](/docs/6.0.0/) of the Graph. The current data are only exposed via the [OpenAIRE Graph API](https://graph.openaire.eu/develop/) and added-value services that are built on top of this version of the Graph (e.g., the [OpenAIRE Explore](https://explore.openaire.eu/)). If you are interested to get bulk access to our latest data, please contact us via our [helpdesk](https://graph.openaire.eu/support).
::: -->
The large size of the OpenAIRE Graph is a major impediment for beginners to familiarise with the underlying data model and explore its contents.
Working with the Graph in its full size typically requires access to a huge distributed computing infrastructure which cannot be easily accessible to everyone.
[The OpenAIRE Beginner’s Kit](https://doi.org/10.5281/zenodo.7490191) aims to address this issue. It consists of two components:
<!-- :::caution
This version is not accompanied with public dataset files, hence the files in this section are based on [v6.0.0](/docs/6.0.0/) of the Graph. The current data are only exposed via the [OpenAIRE Graph API](https://graph.openaire.eu/develop/) and added-value services that are built on top of this version of the Graph (e.g., the [OpenAIRE Explore](https://explore.openaire.eu/)). If you are interested to get bulk access to our latest data, please contact us via our [helpdesk](https://graph.openaire.eu/support).
::: -->
* A subset of the Graph composed of the research products published between 2022-06-29 and 2022-12-29, all the entities connected to them and the respective relationships.
* A Zeppelin notebook that demonstrates how you can use PySpark to analyse the Graph and get answers to some interesting research questions. A guide to Apache Zeppelin can be found [here](https://docs.cloudera.com/HDPDocuments/HDP2/HDP-2.6.5/bk_zeppelin-component-guide/content/ch_overview.html).

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# Sub-graph datasets
<!-- :::caution
This version is not accompanied with public dump files, hence the files in this section are based on [v6.0.0](/docs/6.0.0/) of the Graph. The current data are only exposed via the [OpenAIRE Graph API](https://graph.openaire.eu/develop/) and added-value services that are built on top of this version of the Graph (e.g., the [OpenAIRE Explore](https://explore.openaire.eu/)). If you are interested to get bulk access to our latest data, please contact us via our [helpdesk](https://graph.openaire.eu/support).
::: -->
In order to facilitate users, different datasets are available under the Zenodo community called [OpenAIRE Graph](https://zenodo.org/communities/openaire-research-graph).
This page lists all alternative datasets currently available.
<!-- :::caution
This version is not accompanied with public dataset files, hence the files in this section are based on [v6.0.0](/docs/6.0.0/) of the Graph. The current data are only exposed via the [OpenAIRE Graph API](https://graph.openaire.eu/develop/) and added-value services that are built on top of this version of the Graph (e.g., the [OpenAIRE Explore](https://explore.openaire.eu/)). If you are interested to get bulk access to our latest data, please contact us via our [helpdesk](https://graph.openaire.eu/support).
::: -->
## The OpenAIRE COVID-19 dataset

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docs/graph-production-workflow/aggregation/non-compatible-sources/ebi.md
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@ -69,7 +69,7 @@ curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33024307/datalinks
```
## Mapping
The table below describes the mapping from the EBI links records to the OpenAIRE Graph dump format.
The table below describes the mapping from the EBI links records to the OpenAIRE Graph Dataset format.
We filter all the target links with pid type **ena**, **pdb** or **uniprot**
For each target we construct a Bioentity with the following mapping

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docs/graph-production-workflow/aggregation/non-compatible-sources/uniprot.md
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@ -7,7 +7,7 @@ From this dataset, only the protein records linked to a PubMed publication are e
## Entity Mapping
The table below describes the mapping from the TEXT metadata format to the OpenAIRE Graph dump format.
The table below describes the mapping from the TEXT metadata format to the OpenAIRE Graph Dataset format.
You can check an example of the text metadata [here](https://rest.uniprot.org/uniprotkb/A0A0C5B5G6.txt)
| OpenAIRE Result field path | FASTA record field xpath | Notes |

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docs/publications.md
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# Relevant publications
Open Science services are open and transparent and survive thanks to your active support and to the visibility and reward they gather. If you use one of the [OpenAIRE Graph dumps](https://doi.org/10.5281/zenodo.3516917) for your research, please provide a proper citation following the recommendation that you find on the dump's Zenodo page or as provided below.
Open Science services are open and transparent and survive thanks to your active support and to the visibility and reward they gather. If you use one of the [OpenAIRE Graph Datasets](https://doi.org/10.5281/zenodo.3516917) for your research, please provide a proper citation following the recommendation that you find on the dataset's Zenodo page or as provided below.
:::note How to cite

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static/bibtex/OpenAIRE_Research_Graph_dump.bib
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@ -21,7 +21,7 @@
Vergoulis, Thanasis and
Chatzopoulos, Serafeim and
Pierrakos, Dimitris},
title = {OpenAIRE Research Graph Dump},
title = {OpenAIRE Graph Dataset},
month = dec,
year = 2022,
note = {{A new version of this dataset is published every 6