From 29d3da85f16466cafa64e087bc22a9762741f593 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 25 Nov 2022 17:16:20 +0100 Subject: [PATCH] [EOSC DUMP] added resources needed for the review as test --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 16 +++ .../dhp/oa/graph/raw/zenodo7351221.xml | 118 +++++++++++++++++ .../dhp/oa/graph/raw/zenodo7351393.xml | 119 ++++++++++++++++++ .../dhp/oa/graph/raw/zenodo7353841.xml | 70 +++++++++++ 4 files changed, 323 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351221.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351393.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7353841.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 421c916b0..ed6179cb5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -12,6 +12,7 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import com.fasterxml.jackson.core.JsonProcessingException; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.DocumentException; @@ -991,6 +992,21 @@ class MappersTest { assertTrue(actual.isEmpty()); } + @Test + void testEoscFutureHackZenodo() throws IOException { + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("zenodo7351221.xml"))); + + final List actual = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + actual.forEach(a -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(a)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + } + private void assertValidId(final String id) { // System.out.println(id); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351221.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351221.xml new file mode 100644 index 000000000..3f5ed0ce8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351221.xml @@ -0,0 +1,118 @@ + +> +
+ oai:zenodo.org:7351221 + 2020-01-20T16:45:20Z + openaire + + od______2659::040cee965a4544e343a2ba149783c3fc + 2022-11-25T01:08:31Z +
+ + + 10.5281/zenodo.7351221 + + + Karki, Reagon + Reagon + Karki + 0000-0002-1815-0037 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + + COVID-19 Knowledge Graph: A semantic resource embedding biological and chemical entities + + Zenodo + 2022 + + + Zaliani, Andrea + Andrea + Zaliani + 0000-0002-1740-8390 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + Gadiya, Yojana + Yojana + Gadiya + 0000-0002-7683-0452 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + Gribbon, Philip + Philip + Gribbon + 0000-0001-7655-2459 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + + 2022-11-23 + + + + https://zenodo.org/record/7351221 + + + https://github.com/Fraunhofer-ITMP/BY-COVID-KG + https://github.com/Fraunhofer-ITMP/BY-COVID-KG/blob/main/BY_COVID_update_August.ipynb + 10.5281/zenodo.7351220 + https://zenodo.org/communities/covid-19 + + v1.0.0 + + Open Access + + + <p>A Knowledge graph representation of compounds and associated biological entities in the BY-COVID and EOSC Future project.</p> + + <p><strong>Current status</strong></p> + + <ul> + <li>Number of Nodes: 35952</li> + <li>Number of Edges: 279462</li> + <li>Human Proteins: 1347</li> + <li>Assay: 15835</li> + <li>Chemical/Compound: 4096</li> + <li>Mechanism of Action: 739</li> + <li>Pathway: 1513</li> + <li>Disease: 1585</li> + <li>SideEffect: 7420</li> + <li>Biological Process: 2085</li> + <li>Molecular Function: 1332</li> + </ul> + + <p>Please check the BY_COVID_update_August.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in &#39;data\export&#39; folder.</p> + + <p>&nbsp;</p> + + + + European Commission + 10.13039/100010661 + 101017536 + EOSC Future + + + European Commission + 10.13039/100018693 + 101046203 + Beyond COVID + + + + 10.5281/zenodo.7351221 + 0029 + + OPEN + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351393.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351393.xml new file mode 100644 index 000000000..275dabb12 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7351393.xml @@ -0,0 +1,119 @@ + +> +
+ oai:zenodo.org:7351393 + 2020-01-20T16:45:20Z + openaire + + od______2659::db2bc6381545f80dc9feec808a173ec0 + 2022-11-25T01:08:31Z +
+ + + 10.5281/zenodo.7351393 + + + Karki, Reagon + Reagon + Karki + 0000-0002-1815-0037 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + Andrea, Zaliani + Zaliani + Andrea + 0000-0002-1740-8390 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + Gadiya, Yojana + Yojana + Gadiya + 0000-0002-7683-0452 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + Gribbon, Philip + Philip + Gribbon + 0000-0001-7655-2459 + Fraunhofer Institute of Translation Medicine and Pharmacology + + + + Monkeypox Knowledge Graph: A semantic resource embedding biological and chemical entities + + Zenodo + 2022 + + knowledge graph + monkeypox + systems biology + + + 2022-07-28 + + + + https://zenodo.org/record/7351393 + + + 10.1101/2022.08.02.502453 + https://github.com/Fraunhofer-ITMP/mpox-kg/blob/main/graph.ipynb + 10.5281/zenodo.7351392 + + v1.0.0 + + Open Access + + + <p>The Monkeypox KG is built using viral and human proteins reported in different resources. Additionally, the KG represents chemicals tested against Monkeypox and their targets, associated biological processes, molecular functions, diseases and side effects.</p> + + <p><strong>KG status</strong></p> + + <p>Version 1 stats:</p> + + <ul> + <li>Number of Nodes: 8235</li> + <li>Number of Edges: 40422</li> + </ul> + + <p>Version 2 stats (2nd September) :</p> + + <ul> + <li>Number of Nodes: 9129</li> + <li>Number of Edges: 44568</li> + </ul> + + <p>Please check the graph.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in &#39;data\export&#39; folder.</p> + + <p>&nbsp;</p> + If you use this knowledge graph for your analysis, please cite it using this metadata. + + + + European Commission + 10.13039/100010661 + 101017536 + EOSC Future + + + European Commission + 10.13039/100018693 + 101046203 + Beyond COVID + + + + 10.5281/zenodo.7351393 + 0029 + OPEN + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7353841.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7353841.xml new file mode 100644 index 000000000..ecd020332 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/zenodo7353841.xml @@ -0,0 +1,70 @@ + +> +
+ oai:zenodo.org:7353841 + 2020-01-20T16:45:20Z + openaire + + od______2659::3e4323c221f269e5f3d6db4c61dd2ec8 + 22022-11-24T08:41:37Z +
+ + + 10.5281/zenodo.7353841 + + + Tjerk Krijger + 0000-0002-1722-0523 + MARIS + + + + ENVRI SP - Dashboard State of the Environment - Ocean Indicators + + Zenodo + 2022 + + ENVRI-FAIR + Science Project + Dashboard State of the Environment + EOSC + EOSC-FUTURE + + + 2022-11-24 + + + + https://zenodo.org/record/7353841 + + + 10.5281/zenodo.7353840 + https://zenodo.org/communities/envri + + + Creative Commons Attribution 4.0 International + Open Access + + + <p>The attached .yaml file is used as input to the Dashboard State of the Environment, which is a science project of the ENVRI-FAIR science cluster within EOSC-FUTURE. The contents of the file&nbsp;enable&nbsp;the visualization of&nbsp;Ocean indicators on the dashboard.&nbsp;It is possible to download the attached file and change the contents to include indicators from different domains such as atmosphere or biodiversity.&nbsp;</p> + + + + European Commission + 10.13039/100010661 + 101017536 + EOSC Future + + + + 10.5281/zenodo.7353841 + 0020 + OPEN + + + + \ No newline at end of file