sciknoworg · Krishna-Rani-t · Apr 1, 2026 · Apr 8, 2026 · Apr 8, 2026
diff --git a/docs/source/benchmarking/agriculture/agro.rst b/docs/source/benchmarking/agriculture/agro.rst
@@ -25,29 +25,29 @@
 Agronomy Ontology (AgrO)
 ========================================================================================================
 
+
 The Agronomy Ontology (AgrO) provides terms from the agronomy domain
-that are semantically organized and facilitate the collection, storage,
-and use of agronomic data, enabling easier interpretation and reuse by
-both humans and machines [#cgiar]_ [#obo]_. To analyze the effects of
-varying practices within cropping systems, it is often necessary to
-integrate data from multiple disciplinary domains. For example, data on
-field management, soil, weather, and crop phenotypes may need to be
-combined to assess crop performance under different management
-interventions. However, agronomic data are often collected, described,
-and stored in inconsistent ways, which impedes data comparison, mining,
-interpretation, and reuse [#cgiar]_. The use of standards for metadata
-and data annotation plays a key role in addressing these challenges.
-While the CG Core Metadata Schema provides a metadata standard to
-describe agricultural datasets, the Agronomy Ontology enables the
-description of agronomic variables using standardized and semantically
-defined terms [#cgiar]_ [#agrofims]_. AgrO specifically covers agronomic
-practices, techniques, and variables used in agronomic experiments and
-reuses terms from other ontologies to support interoperability [#obo]_.
-
-**Example Usage**: Annotate agronomic field experiment data with AgrO terms for management
-practices, treatments, and measured variables to enable standardized
-description, interoperable storage, and cross-study comparison of
-agricultural data [#obo]_ [#agrofims]_.
+that are semantically organized to support the collection, integration,
+and reuse of agronomic data across disciplinary domains [#agro]_.
+To analyze the effects of varying practices within cropping systems, it
+is often necessary to integrate data from multiple disciplinary domains,
+including field management, soil, weather, and crop phenotype data.
+AgrO was developed to address the inconsistent description and storage
+of agronomic data, which can hinder comparison, interpretation, and
+reuse across studies and information systems [#agro]_. The use of
+standards for metadata and data annotation plays a key role in
+addressing these challenges. AgrO enables the description of agronomic
+variables using standardized and semantically defined terms and covers
+agronomic practices, techniques, and variables used in agronomic
+experiments [#agro]_. The ontology is available through AgroPortal for
+browsing and access [#agroportal]_.
+
+**Example Usage**: Annotate agronomic field experiment data with AgrO
+terms for management practices, treatments, and measured variables to
+support standardized description, improved interoperability, and
+cross-study comparison across agricultural datasets [#agro]_
+[#agroportal]_.
+
 
 Metrics & Statistics
 --------------------------
@@ -160,11 +160,20 @@ Use the following code to import this ontology programmatically:
 References
 ----------
 
-.. [#cgiar] CGIAR. n.d. "Agronomy Ontology."
-   Available at: https://bigdata.cgiar.org/resources/agronomy-ontology/
+.. [#agro] Devare, M., Aubert, C., Laporte, M.-A., Valette, L.,
+   Arnaud, E., and Buttigieg, P. L. 2016.
+   "Data-driven Agricultural Research for Development:
+   A Need for Data Harmonization Via Semantics."
+   In *Proceedings of the 7th International Conference on
+   Biomedical Ontology (ICBO 2016)*.
+   CEUR Workshop Proceedings, Vol. 1747.
+   Available at:
+   https://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
 
-.. [#obo] OBO Foundry. n.d. "Agronomy Ontology (AGRO)."
-   Available at: https://obofoundry.org/ontology/agro.html
+.. [#agroportal] Devare, M., Aubert, C., Laporte, M.-A., Valette, L.,
+   Arnaud, E., and Buttigieg, P. L. n.d. "Agronomy Ontology (AgrO)."
+   Available at:
+   https://agroportal.lirmm.fr/ontologies/AGRO?p=summary
 
 .. [#agrofims] Devare, M., Aubert, C., Benites Alfaro, O. E.,
    Perez Masias, I. O., and Laporte, M.-A. 2021.

diff --git a/docs/source/benchmarking/agriculture/agrovoc.rst b/docs/source/benchmarking/agriculture/agrovoc.rst
@@ -25,26 +25,26 @@ AGROVOC Multilingual Thesaurus (AGROVOC)
 
 AGROVOC is a multilingual thesaurus and Linked Open Data resource
 developed and maintained by the Food and Agriculture Organization (FAO)
-of the United Nations [#fao-home]_ [#agrovoc-paper]_. It provides a
+of the United Nations [#fao-home]_ [#linked-dataset]_. It provides a
 structured collection of agricultural concepts, terms, definitions, and
 relationships that support unambiguous resource identification,
-standardized indexing, and more efficient search [#fao-home]_. As a
-multilingual knowledge organization system, AGROVOC facilitates access
-to agricultural information across domains and languages [#fao-home]_
-[#agrovoc-paper]_. It covers concepts relevant to food, agriculture,
-fisheries, forestry, environment, and related domains, and supports
-semantic interoperability through hierarchical and associative
+standardized indexing, and more efficient search [#fao-home]_.
+As a multilingual knowledge organization system, AGROVOC facilitates
+access to agricultural information across domains and languages
+[#fao-home]_ [#linked-dataset]_. It covers concepts relevant to food,
+agriculture, fisheries, forestry, environment, and related domains, and
+supports semantic interoperability through hierarchical and associative
 relationships as well as links to other vocabularies and datasets
-[#fao-home]_ [#linked-dataset]_. With over 41,000 concepts and extensive
-multilingual term coverage, AGROVOC is widely used for data annotation,
-knowledge organization, and information retrieval in agricultural and
-food-related information systems [#fao-dpg]_ [#agrovoc-paper]_.
+[#fao-home]_ [#linked-dataset]_. AGROVOC is widely used for data
+annotation, knowledge organization, and information retrieval in
+agricultural and food-related information systems [#fao-home]_
+[#linked-dataset]_.
 
-**Example Usage**: Annotate a multilingual agricultural dataset with AGROVOC concepts for
-crops, soil types, pests, livestock, and farming practices to enable
-standardized indexing, semantic interoperability, and cross-language
-search across international agricultural databases and repositories
-[#fao-home]_ [#agrovoc-paper]_.
+**Example Usage**: Annotate a multilingual agricultural dataset with
+AGROVOC concepts for crops, soil types, pests, livestock, and farming
+practices to enable standardized indexing, semantic interoperability,
+and cross-language search across agricultural databases and repositories
+[#fao-home]_ [#linked-dataset]_.
 
 Metrics & Statistics
 --------------------------
@@ -158,22 +158,12 @@ References
 ----------
 
 .. [#fao-home] Food and Agriculture Organization of the United Nations
-   (FAO). n.d. "AGROVOC." Available at:
+   (FAO). n.d. "AGROVOC."
+   Available at:
    https://www.fao.org/agrovoc/
 
-.. [#agrovoc-paper] Subirats-Coll, I., Kolshus, K., Turbati, A.,
-   Stellato, A., Mietzsch, E., Martini, D., and Zeng, M. 2022.
-   "AGROVOC: The linked data concept hub for food and agriculture."
-   *Computers and Electronics in Agriculture* 196:105965.
-   doi:10.1016/j.compag.2020.105965
-
 .. [#linked-dataset] Caracciolo, C., Stellato, A., Morshed, A.,
    Johannsen, G., Rajbhandari, S., Jaques, Y., and Keizer, J. 2013.
    "The AGROVOC Linked Dataset." *Semantic Web* 4(3):341-348.
    Available at:
    https://www.fao.org/agrovoc/publications/agrovoc-linked-dataset
-
-.. [#fao-dpg] Food and Agriculture Organization of the United Nations
-   (FAO). 2024. "AGROVOC is now a certified Digital Public Good!"
-   Available at:
-   https://www.fao.org/agora/news/agrovoc-now-certified-digital-public-good
diff --git a/docs/source/benchmarking/agriculture/atol.rst b/docs/source/benchmarking/agriculture/atol.rst
@@ -161,8 +161,9 @@ References
 .. [#inra] INRAE Open Data. n.d. "Animal Trait Ontology for Livestock."
    Available at: https://opendata.inra.fr/ATOL/page/
 
-.. [#agroportal] AgroPortal. n.d. "ATOL | Summary."
-   Available at: https://agroportal.lirmm.fr/ontologies/ATOL
+.. [#agroportal] AgroPortal. n.d. "Animal Trait Ontology for Livestock (ATOL)."
+   Available at:
+   https://agroportal.lirmm.fr/ontologies/ATOL
 
 .. [#atol-paper] Golik, W., Dameron, O., Bugeon, J., Fatet, A., Hue, I.,
    Hurtaud, C., Reichstadt, M., Salaün, M.-C., Vernet, J., Joret, L.,

diff --git a/docs/source/benchmarking/agriculture/po.rst b/docs/source/benchmarking/agriculture/po.rst
@@ -30,25 +30,22 @@ resource that links plant anatomy, morphology, growth, and development
 to plant genomics and phenomics data [#obo]_ [#po-paper]_. Developed as
 a community resource, PO provides a framework for describing plant
 structures and developmental stages across plant species [#obo]_
-[#po-dev-paper]_. The ontology integrates anatomical and developmental
+[#po-paper]_. The ontology integrates anatomical and developmental
 terms that can be associated with plant genes and phenotypes, enabling
 researchers to annotate data and support comparative genomics and
-comparative plant biology [#po-paper]_ [#po-dev-paper]_. PO is designed
-to facilitate data integration and interoperability in plant science
-research [#obo]_ [#po-paper]_. With its hierarchical organization of
-plant structures and developmental stages, including whole plants,
-organs, tissues, and cell types, PO supports applications such as
-literature curation, genome annotation, and phenotypic data annotation
-[#po-paper]_. The ontology is under active development and is integrated
-with the Planteome project and other biological ontologies to support
-semantic compatibility in the plant science community [#obo]_
-[#planteome]_.
-
-**Example Usage**: Annotate a plant genomics or phenomics dataset with PO terms for plant
-structures and developmental stages, such as leaf, root, flower, seed,
-or senescent stage, to enable standardized annotation, cross-species
-comparison, and integration with plant science databases and analysis
-platforms [#obo]_ [#po-paper]_.
+comparative plant biology [#po-paper]_. PO is designed to facilitate
+data integration and interoperability in plant science research
+[#obo]_ [#po-paper]_. With its hierarchical organization of plant
+structures and developmental stages, including whole plants, organs,
+tissues, and cell types, PO supports applications such as literature
+curation, genome annotation, and phenotypic data annotation
+[#po-paper]_.
+
+**Example Usage**: Annotate a plant genomics or phenomics dataset with
+PO terms for plant structures and developmental stages, such as leaf,
+root, flower, seed, or senescent stage, to enable standardized
+annotation, cross-species comparison, and integration with plant
+science databases and analysis platforms [#obo]_ [#po-paper]_.
 
 Metrics & Statistics
 --------------------------
@@ -171,18 +168,3 @@ References
    *Plant and Cell Physiology* 54(2): e1.
    doi:10.1093/pcp/pcs163
    Available at: `https://pmc.ncbi.nlm.nih.gov/articles/PMC3583023/ <https://pmc.ncbi.nlm.nih.gov/articles/PMC3583023/>`_
-
-.. [#po-dev-paper] Walls, R. L., Cooper, L., Elser, J., Gandolfo, M. A.,
-   Mungall, C. J., Smith, B., Stevenson, D. W., and Jaiswal, P. 2019.
-   "The Plant Ontology Facilitates Comparisons of Plant Development
-   Stages Across Species."
-   *Frontiers in Plant Science* 10:631.
-   doi:10.3389/fpls.2019.00631
-   Available at: `https://pmc.ncbi.nlm.nih.gov/articles/PMC6558174/ <https://pmc.ncbi.nlm.nih.gov/articles/PMC6558174/>`_
-
-.. [#planteome] Cooper, L., Elser, J., Laporte, M.-A., Arnaud, E.,
-   and Jaiswal, P. 2024. "Planteome 2024 Update: Reference Ontologies
-   and Knowledgebase for Plant Biology."
-   *Nucleic Acids Research* 52(D1): D1548-D1555.
-   doi:10.1093/nar/gkad1028
-   Available at: `https://pmc.ncbi.nlm.nih.gov/articles/PMC10767901/ <https://pmc.ncbi.nlm.nih.gov/articles/PMC10767901/>`_
diff --git a/docs/source/benchmarking/arts_and_humanities/chordontology.rst b/docs/source/benchmarking/arts_and_humanities/chordontology.rst
@@ -25,28 +25,32 @@
 Chord Ontology (ChordOntology)
 ========================================================================================================
 
-The Chord Ontology is a formal representation for describing and classifying
-chords and chord sequences in musical resources. It provides a structured
-vocabulary for representing harmonic concepts and chord structures, enabling
-semantic annotation and analysis of music data. The ontology captures core
-chord properties including chord type (for example major, minor, diminished,
-and augmented), root note, constituent intervals, and bass note. It supports
-the annotation of audio files, musical scores, and symbolic music files by
-linking chord events to temporal structures and music resources. The ontology
-was developed within the OMRAS2 project and is designed to interoperate with
-related Semantic Web resources such as the Music Ontology, Timeline Ontology,
-and Event Ontology. By formalizing chord relationships and structures, the
-Chord Ontology supports computational music analysis, harmonic annotation,
-music information retrieval, and digital musicology applications. It provides
-a common framework for music annotation across datasets and tools, supporting
+The Chord Ontology is a formal representation for describing and
+classifying chords and chord sequences in musical resources
+[#chord-spec]_. It provides a structured vocabulary for representing
+harmonic concepts and chord structures, enabling semantic annotation and
+analysis of music data [#chord-spec]_. The ontology captures core chord
+properties including chord type, such as major, minor, diminished, and
+augmented, as well as root note, constituent intervals, and bass note
+[#chord-spec]_. It supports the annotation of audio files, musical
+scores, and symbolic music files by linking chord events to temporal
+structures and music resources [#chord-spec]_. The ontology was
+developed within the OMRAS2 project and is designed to interoperate with
+related Semantic Web resources such as the Music Ontology, Timeline
+Ontology, and Event Ontology [#chord-spec]_. By formalizing chord
+relationships and structures, the Chord Ontology supports computational
+music analysis, harmonic annotation, music information retrieval, and
+digital musicology applications [#chord-spec]_. It provides a common
+framework for music annotation across datasets and tools, supporting
 harmonic analysis, corpus annotation, and music information systems
-development [#chord-spec]_ [#omras2]_ [#music-ontology]_.
+development [#chord-spec]_.
 
 **Example Usage**: Annotate the harmonic timeline of an audio recording,
-musical score, or symbolic music file with Chord Ontology terms for chord
-events, root notes, intervals, and bass notes to enable semantic search,
-computational harmonic analysis, and integration with music information
-retrieval datasets and tools [#chord-spec]_ [#omras2]_.
+musical score, or symbolic music file with Chord Ontology terms for
+chord events, root notes, intervals, and bass notes to enable semantic
+search, computational harmonic analysis, and integration with music
+information retrieval datasets and tools [#chord-spec]_.
+
 
 Metrics & Statistics
 --------------------------
@@ -162,17 +166,4 @@ References
 .. [#chord-spec] Sutton, C., Raimond, Y., and Mauch, M. 2007.
    "Chord Ontology Specification."
    OMRAS2 Project, Centre for Digital Music, Queen Mary University of London.
-   Available at: http://purl.org/ontology/chord/
-   Also available at: https://motools.sourceforge.net/chord_draft_1/chord.html
-
-.. [#omras2] Fazekas, G., Raimond, Y., Jacobson, K., and Sandler, M. 2010.
-   "An Overview of Semantic Web Activities in the OMRAS2 Project."
-   *Journal of New Music Research* 39(4): 295-311.
-   doi:10.1080/09298215.2010.536555
-
-.. [#music-ontology] Raimond, Y., Abdallah, S. A., Sandler, M. B.,
-   and Giasson, F. 2007.
-   "The Music Ontology."
-   In *Proceedings of the 8th International Conference on Music Information
-   Retrieval (ISMIR 2007)*, Vienna, Austria, pp. 417-422.
-   Available at: https://ismir2007.ismir.net/proceedings/ISMIR2007_p417_raimond.pdf
+   Available at: https://motools.sourceforge.net/chord_draft_1/chord.html
diff --git a/docs/source/benchmarking/arts_and_humanities/icon.rst b/docs/source/benchmarking/arts_and_humanities/icon.rst
@@ -164,6 +164,10 @@ Use the following code to import this ontology programmatically:
 References
 ----------
 
+.. [#icon-doc] ICON Ontology Documentation. n.d.
+   "ICON Ontology Documentation 2.0."
+   Available at: https://br0ast.github.io/ICON/ICONOntologyDocumentation2.0/index-en.html
+
 .. [#icon-paper] Sartini, B., Baroncini, S., van Erp, M., Tomasi, F.,
    and Gangemi, A. 2023. "ICON: An Ontology for Comprehensive Artistic
    Interpretations."
@@ -176,8 +180,4 @@ References
    In *Proceedings of the Semantic Web and Ontology Design for Cultural
    Heritage Workshop (SWODCH 2023)*.
    CEUR Workshop Proceedings 3540.
-   Available at: `https://ceur-ws.org/Vol-3540/paper4.pdf <https://ceur-ws.org/Vol-3540/paper4.pdf>`_
-
-.. [#icon-doc] ICON Ontology Documentation. n.d.
-   "ICON Ontology Documentation 2.0."
-   Available at: `https://br0ast.github.io/ICON/ICONOntologyDocumentation2.0/index-en.html <https://br0ast.github.io/ICON/ICONOntologyDocumentation2.0/index-en.html>`_
+   Available at: https://ceur-ws.org/Vol-3540/paper4.pdf