Merge pull request #54 from MarkusSchilling/main

Update Readme

Author: MarkusSchilling

microscopy_ontology_MO/README.md

@@ -1,7 +1,31 @@
 # Microscopy Ontology (MO)
-This repository contains the [Microscopy Ontology (MO)](https://github.com/materialdigital/application-ontologies/blob/main/microscopy_ontology_MO/pmd_mo.ttl) and other relevant information. The MO has been developed as part of the Platform MaterialDigital [(PMD)](https://materialdigital.de/) project in collaboration with the National Institute of Standards and Technology [(NIST)](https://www.nist.gov/).
+This repository contains the [Microscopy Ontology (MO)](https://github.com/materialdigital/application-ontologies/blob/main/microscopy_ontology_MO/pmd_mo.ttl) and related information. The MO has been developed as part of the Platform MaterialDigital [(PMD)](https://materialdigital.de/) project in collaboration with the National Institute of Standards and Technology ([NIST](https://www.nist.gov/)).
 
-Designed as an application ontology, the MO imports and builds upon the PMD Core Ontology ([PMDco](https://github.com/materialdigital/core-ontology/tree/main)), a mid-level ontology for materials science and engineering ([more details here](https://doi.org/10.1016/j.matdes.2023.112603)), and extends the PMDco with approx. 200 terms retrieved from an NLP approach by analyzing 2 decades of [Microscopy and Microanalysis Conference](https://microscopy.org/past-m-m-meetings) proceedings. 
+Designed as an application ontology, the MO imports and builds upon the PMD Core Ontology ([PMDco](https://github.com/materialdigital/core-ontology/tree/main)), a mid-level ontology for materials science and engineering ([more details here](https://doi.org/10.1016/j.matdes.2023.112603)), and extends the PMDco with approx. 200 terms retrieved from an NLP approach by analyzing 2 decades of [Microscopy and Microanalysis Conference](https://microscopy.org/past-m-m-meetings) proceedings.
+
+For further details, see:
+
+### Scientific Publication
+
+When using and referring to the Microscopy Ontology (MO), please cite the following publication, which provides comprehensive details and the foundational rationale behind the development of this ontology:
+
+*Bayerlein, B., Schilling, M., Curran, M. et al. Natural Language Processing-Driven Microscopy Ontology Development. Integr Mater Manuf Innov (2024). https://doi.org/10.1007/s40192-024-00378-y*
+
+Bibtex:
+```
+@article{Bayerlein2024,
+  author = {Bernd Bayerlein and Markus Schilling and Maurice Curran and Carelyn E. Campbell and Alden A. Dima and Henk Birkholz and June W. Lau},
+  title = {Natural Language Processing-Driven Microscopy Ontology Development},
+  journal = {Integrating Materials and Manufacturing Innovation},
+  year = {2024},
+  doi = {10.1007/s40192-024-00378-y},
+  url = {https://doi.org/10.1007/s40192-024-00378-y},
+  issn = {2193-9772}
+}
+```
+available open access at: [Integrating Materials and Manufacturing Innovation](https://doi.org/10.1007/s40192-024-00378-y).
+
+**Note: This repository contains the PROV-O compatible MO version (referring to [PMDco 2.0.8](https://github.com/materialdigital/core-ontology/releases/tag/v2.0.8)). For the newest BFO-compatible MO version, please refer to the [microscopy ontology repository](https://github.com/materialdigital/microscopy-ontology).**
 
 ## Scope 
 The Microscopy Ontology (MO) extends the ontological framework of the PMDco v2.0.7 as an [application ontology](https://github.com/materialdigital/application-ontologies). The MO facilitates semantic integration and the interoperable connection of diverse data sources from the fields of microscopy and microanalysis. Consequently, the MO paves the way for new, adaptable data applications and analyses across various experiments and studies ([Click here for more info](10.1038/s41597-024-03169-4)).
@@ -22,11 +46,6 @@ An HTML documentation of MO that was auto-generated using [Widoco tool](https://
 ## Contribute
 An open [MO HackMD document](https://hackmd.io/21tFuZTITq2draxRPbepzg) used for collaborative work on shared vocabulary / thesaurus used for [pmd_mo.ttl](https://github.com/materialdigital/application-ontologies/blob/main/microscopy_ontology_MO/pmd_mo.ttl) is available. Please feel free to contribute but highlight changes in the thesaurus.
 
-## Publication | Citation
-When using and referring to the Microscopy Ontology (MO), please cite the following publication, which provides comprehensive details and the foundational rationale behind the development of this ontology:
-
-"available soon"
-
 ## Namespaces
 In this section, the namespaces used in the Microscopy Ontology (MO) are listed. These can also be found in the [pmd_mo.ttl file](https://github.com/materialdigital/application-ontologies/blob/main/microscopy_ontology_MO/pmd_mo.ttl).
 Since MO imports the PMDco, the PMDco namespace (https://w3id.org/pmd/co/) is used for higher-level ontological concepts.

microscopy_ontology_MO/catalog-v001.xml

@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri id="Imports Wizard Entry" name="https://w3id.org/pmd/co/3.0.0-dev" uri="https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/develop-3.0.0/pmdco.owl"/>
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
 </catalog>

tensile_test_ontology_TTO/catalog-v001.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
+</catalog>