Hi Knowledge KB - User contributions [en]

Sites:WWW/Tools/Hypothesis networks/page

2024-12-14T08:40:22Z

JonathanJeschke: /* Invasion biology: large hypothesis network */

Hypothesis networks map major hypotheses. They structure and provide an overview of existing theory. Through the hierarchy-of-hypotheses approach ([https://doi.org/10.3897/neobiota.14.3435 Jeschke et al. 2012], [https://doi.org/10.1007/s13280-012-0379-x Heger et al. 2013], [https://doi.org/10.1093/biosci/biaa130 Heger et al. 2021]), hypothesis networks can be hierarchically structured and connected to empirical studies and data. Thus far, we have created several hypothesis networks, two of them are available as hierarchical interactive networks that can be interactively explored (other hypothesis networks in invasion biology, which were created by other methods, are available in [https://doi.org/10.1002/ecs2.2146 Enders et al. 2018] and [https://doi.org/10.3897/neobiota.47.32608 Enders et al. 2019]):


== Invasion biology: large hypothesis network ==

[[File:Invasion biology large hypothesis network.png|center|link=https://v2020.hi-knowledge.org/invasion-biology-large/]]

[https://v2020.hi-knowledge.org/invasion-biology-large/ Interactive, hierarchically structured network] showing clusters of 39 invasion hypotheses, based on [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] and the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). The hierarchical structure was achieved by applying the hierarchy-of-hypotheses approach. This tool is an extension of the smaller network with 12 hypotheses.



== Invasion biology: hypothesis network book ==

[[File:Invasion biology hypothesis network book.png|center|link=https://hi-knowledge.org/invasion-biology/]]

[[File:HiK promo.webm|center|800x450px|Hypothesis Network Video]]

An [https://hi-knowledge.org/invasion-biology/ interactive visualisation tool] that structures scientific evidence from ca. 1100 publications in a hierarchical network of 12 invasion hypotheses, based on the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]).

== Urban ecology: bipartite hypothesis network ==

[[File:Bipartite Hypothesis Network for Urban Ecology.webp|alt=Bipartite Hypothesis Network for Urban Ecology|center|link=https://doi.org/10.1111/brv.12964]]

Bipartite network of hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)], which are also available in a [https://www.wikidata.org/wiki/Wikidata:WikiProject_Ecology/Task_Force_Urban_Ecology Wikiproject].

== Invasion biology meets urban ecology: combined hypothesis network ==

[[File:Combined urban and invasion hypothesis networks.webp|alt=Forced directed graph of categories and hypotheses in urban and invasion biology|center|link=https://rpubs.com/maudbv/urban-invasion-network]]

[https://rpubs.com/maudbv/urban-invasion-network Interactive visualisation of a combined hypothesis network covering both invasion biology and urban ecology] (cf. [https://doi.org/10.3897/rio.9.e115395 Bernard-Verdier et al. 2023]). This network combines hypotheses in invasion biology from [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] with hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)].

Sites:WWW/Tools/Hypothesis networks/page

2024-12-14T08:39:12Z

JonathanJeschke: /* Invasion biology: large hypothesis network */

Hypothesis networks map major hypotheses. They structure and provide an overview of existing theory. Through the hierarchy-of-hypotheses approach ([https://doi.org/10.3897/neobiota.14.3435 Jeschke et al. 2012], [https://doi.org/10.1007/s13280-012-0379-x Heger et al. 2013], [https://doi.org/10.1093/biosci/biaa130 Heger et al. 2021]), hypothesis networks can be hierarchically structured and connected to empirical studies and data. Thus far, we have created several hypothesis networks, two of them are available as hierarchical interactive networks that can be interactively explored (other hypothesis networks in invasion biology, which were created by other methods, are available in [https://doi.org/10.1002/ecs2.2146 Enders et al. 2018] and [https://doi.org/10.3897/neobiota.47.32608 Enders et al. 2019]):


== Invasion biology: large hypothesis network ==

[[File:Invasion biology large hypothesis network.png|center|link=https://hi-knowledge.org/invasion-biology-large/]]

[https://v2020.hi-knowledge.org/invasion-biology-large/ Interactive, hierarchically structured network] showing clusters of 39 invasion hypotheses, based on [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] and the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). The hierarchical structure was achieved by applying the hierarchy-of-hypotheses approach. This tool is an extension of the smaller network with 12 hypotheses.



== Invasion biology: hypothesis network book ==

[[File:Invasion biology hypothesis network book.png|center|link=https://hi-knowledge.org/invasion-biology/]]

[[File:HiK promo.webm|center|800x450px|Hypothesis Network Video]]

An [https://hi-knowledge.org/invasion-biology/ interactive visualisation tool] that structures scientific evidence from ca. 1100 publications in a hierarchical network of 12 invasion hypotheses, based on the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]).

== Urban ecology: bipartite hypothesis network ==

[[File:Bipartite Hypothesis Network for Urban Ecology.webp|alt=Bipartite Hypothesis Network for Urban Ecology|center|link=https://doi.org/10.1111/brv.12964]]

Bipartite network of hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)], which are also available in a [https://www.wikidata.org/wiki/Wikidata:WikiProject_Ecology/Task_Force_Urban_Ecology Wikiproject].

== Invasion biology meets urban ecology: combined hypothesis network ==

[[File:Combined urban and invasion hypothesis networks.webp|alt=Forced directed graph of categories and hypotheses in urban and invasion biology|center|link=https://rpubs.com/maudbv/urban-invasion-network]]

[https://rpubs.com/maudbv/urban-invasion-network Interactive visualisation of a combined hypothesis network covering both invasion biology and urban ecology] (cf. [https://doi.org/10.3897/rio.9.e115395 Bernard-Verdier et al. 2023]). This network combines hypotheses in invasion biology from [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] with hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)].

Sites:WWW/Tools/ORKG/page

2024-07-18T07:15:45Z

JonathanJeschke: /* Description: */

= Semantic annotation of literature using ORKG =

== Description: ==

Open platform, templates and database for community-curated and FAIR semantic annotation of the scientific literature. Find out more at: [https://orkg.org orkg.org]

The Open Research Knowledge Graph (ORKG) is a public project hosted by [https://www.tib.eu/en/ TiB Leibniz Information Center for Science and Technology University Library]

== Purpose: ==

* Add your own papers and annotate them in a machine-interpretable way to increase findability and re-use of your work
* Use the ORKG templates to systematically annotate papers for meta-analysis
* Create on-demand interactive syntheses of the literature

== About ==

Authors are the best people to tell us what their study and data are about, and they do it very well for humans reading their papers. However, there is no standardised approach to summarise essential characteristics of papers in a way that is machine interpretable and interoperable. Huge efforts have been made to standardise metadata for datasets (e.g. EML), or to standardise bibliometric information, but nothing for annotating the scientific scope and knowledge contained in publications themselves.

The ORKG makes scientific knowledge human- and machine-actionable and thus enables completely new ways of machine assistance. With the ORKG, authors, but also readers assembling papers for a meta-analysis for instance, can annotate the scientific scope and content of studies. This will help researchers find relevant contributions to their field and create state-of-the-art comparisons and reviews.

== ORKG templates for Ecology and Invasion Biology ==

In collaboration with the ORKG, we established a set of semantic templates to guide ecologists in annotating papers in a machine-interpretable and standardised way. We built these templates in an iterative process in a series of Hi Knowledge workshops (LINKS to workshops).

Semantic templates promise:

* Guidance for ecologists to choose which concepts are important to annotate
* Standardisation of annotations (allowing for controlled vocabulary, handling of synonymy, homonymy, different languages, etc.)
* Flexibility by handling heterogeneity in entries (e.g. different taxonomic levels, different units)
* Machine-interpretable and open metadata to replace publisher keywords
* Re-usability of annotations in future meta-analysis

These templates range from a very broad ecological scoping of a study ('''#1'''), similar to what is usually included in a publication's keywords, to more detailed description of study systems ('''#2''') and study designs ('''#3''').

We also designed templates specific to invasion biology studies. The first ('''#4''') is a general description of the main theme, research questions, hypotheses and invasive taxa investigated, following our current conceptual scheme for invasion biology (internal link to tool). The second ('''#3''') describes the testing of major hypotheses in the field (described by template '''#6'''). It provides information about support or rebuttal of those hypotheses, in the same way as the Hi Knowledge data provided (internal link to hyp network).

'''Table 1:''' ORKG templates created for ecology studies, with #4-6 being specific to invasion biology.

{|
!width="3%"| '''#'''
!width="18%"| '''Template name'''
!width="11%"| '''Domain'''
!width="54%"| '''Description'''
!width="11%"| '''ORKG ID'''
|-
| 1
| '''Study in Ecology and Evolution''' (main template)
| Ecology
| General template for any study in the field of ecology (''sensu largo).'' Includes: research field, approach, taxonomic coverage, geographic coverage, temporal coverage, habitat, etc.
| [https://orkg.org/template/R593657 R593657]
|-
| 2
| '''Ecological study system description'''
| Ecology
| Describes the properties of a specific ecological study system, which can be shared by multiple studies.
| [https://orkg.org/template/R593670 R593670]
|-
| 3
| '''Ecological study design description'''
| Ecology
| Describes the study design (sample size, treatment, etc.) in an ecological study.
| [https://orkg.org/template/R593806 R593806]
|-
| 4
| '''Invasion biology study research question'''
| Invasion biology
| Classifies the study by theme, research question, hypotheses and invasive taxa, following the scheme by Musseau et al. (in prep)
| [https://orkg.org/template/R593830 R593830]
|-
| 5
| '''Hypothesis test in invasion biology'''
| Invasion biology
| Annotate whether the study supports or not a major hypothesis
| [https://orkg.org/template/R646660 R646660]
|-
| 6
| '''Hypotheses in invasion biology template'''
| Invasion biology
| Template for describing major theoretical hypotheses in invasion biology
| [https://orkg.org/template/R602693 R602693]
|}

''Anyone can create a template in the ORKG!''

If you think these templates are insufficient and want to create a template for your field or a particular research question, get started [https://orkg.org/about/19/Templates here].

== Example application: On-demand interactive synthesis for invasion biology ==

Annotations in the ORKG can be [https://orkg.org/data extracted] and used to build interactive syntheses and visualisations on a topic of interest. The easiest way to do this is to first build a comparison table across papers, choose which properties should be compared, and extract this structured data to be ingested in an R shiny app or Jupyter notebook.

As a proof-of-concept, we created an R shiny app from ORKG annotations for the Hi Knowledge dataset on 10 major hypotheses in invasion biology (Jeschke & Heger, 2018). Explore the webapp here:

[https://maudbernardverdier.shinyapps.io/Hypothesis-evidence-explorer/ Hypothesis evidence explorer]

== Example application: Teaching ecology ==

[https://orkg.org/list/R674168/ ORKG list - Class assignment: annotating papers in invasion biology]

Sites:WWW/Tools/ORKG/page

2024-07-18T07:13:42Z

JonathanJeschke: /* Semantic annotation of literature using Open Knowledge Research Graph */

= Semantic annotation of literature using ORKG =

== Description: ==

Open platform, templates and database for community-curated and FAIR semantic annotation of the scientific literature. Find out more at: [https://orkg.org orkg.org]

The ORKG is a public project hosted by [https://www.tib.eu/en/ TiB Leibniz Information Center for Science and Technology University Library]

== Purpose: ==

* Add your own papers and annotate them in a machine-interpretable way to increase findability and re-use of your work
* Use the ORKG templates to systematically annotate papers for meta-analysis
* Create on-demand interactive syntheses of the literature

== About ==

Authors are the best people to tell us what their study and data are about, and they do it very well for humans reading their papers. However, there is no standardised approach to summarise essential characteristics of papers in a way that is machine interpretable and interoperable. Huge efforts have been made to standardise metadata for datasets (e.g. EML), or to standardise bibliometric information, but nothing for annotating the scientific scope and knowledge contained in publications themselves.

The ORKG makes scientific knowledge human- and machine-actionable and thus enables completely new ways of machine assistance. With the ORKG, authors, but also readers assembling papers for a meta-analysis for instance, can annotate the scientific scope and content of studies. This will help researchers find relevant contributions to their field and create state-of-the-art comparisons and reviews.

== ORKG templates for Ecology and Invasion Biology ==

In collaboration with the ORKG, we established a set of semantic templates to guide ecologists in annotating papers in a machine-interpretable and standardised way. We built these templates in an iterative process in a series of Hi Knowledge workshops (LINKS to workshops).

Semantic templates promise:

* Guidance for ecologists to choose which concepts are important to annotate
* Standardisation of annotations (allowing for controlled vocabulary, handling of synonymy, homonymy, different languages, etc.)
* Flexibility by handling heterogeneity in entries (e.g. different taxonomic levels, different units)
* Machine-interpretable and open metadata to replace publisher keywords
* Re-usability of annotations in future meta-analysis

These templates range from a very broad ecological scoping of a study ('''#1'''), similar to what is usually included in a publication's keywords, to more detailed description of study systems ('''#2''') and study designs ('''#3''').

We also designed templates specific to invasion biology studies. The first ('''#4''') is a general description of the main theme, research questions, hypotheses and invasive taxa investigated, following our current conceptual scheme for invasion biology (internal link to tool). The second ('''#3''') describes the testing of major hypotheses in the field (described by template '''#6'''). It provides information about support or rebuttal of those hypotheses, in the same way as the Hi Knowledge data provided (internal link to hyp network).

'''Table 1:''' ORKG templates created for ecology studies, with #4-6 being specific to invasion biology.

{|
!width="3%"| '''#'''
!width="18%"| '''Template name'''
!width="11%"| '''Domain'''
!width="54%"| '''Description'''
!width="11%"| '''ORKG ID'''
|-
| 1
| '''Study in Ecology and Evolution''' (main template)
| Ecology
| General template for any study in the field of ecology (''sensu largo).'' Includes: research field, approach, taxonomic coverage, geographic coverage, temporal coverage, habitat, etc.
| [https://orkg.org/template/R593657 R593657]
|-
| 2
| '''Ecological study system description'''
| Ecology
| Describes the properties of a specific ecological study system, which can be shared by multiple studies.
| [https://orkg.org/template/R593670 R593670]
|-
| 3
| '''Ecological study design description'''
| Ecology
| Describes the study design (sample size, treatment, etc.) in an ecological study.
| [https://orkg.org/template/R593806 R593806]
|-
| 4
| '''Invasion biology study research question'''
| Invasion biology
| Classifies the study by theme, research question, hypotheses and invasive taxa, following the scheme by Musseau et al. (in prep)
| [https://orkg.org/template/R593830 R593830]
|-
| 5
| '''Hypothesis test in invasion biology'''
| Invasion biology
| Annotate whether the study supports or not a major hypothesis
| [https://orkg.org/template/R646660 R646660]
|-
| 6
| '''Hypotheses in invasion biology template'''
| Invasion biology
| Template for describing major theoretical hypotheses in invasion biology
| [https://orkg.org/template/R602693 R602693]
|}

''Anyone can create a template in the ORKG!''

If you think these templates are insufficient and want to create a template for your field or a particular research question, get started [https://orkg.org/about/19/Templates here].

== Example application: On-demand interactive synthesis for invasion biology ==

Annotations in the ORKG can be [https://orkg.org/data extracted] and used to build interactive syntheses and visualisations on a topic of interest. The easiest way to do this is to first build a comparison table across papers, choose which properties should be compared, and extract this structured data to be ingested in an R shiny app or Jupyter notebook.

As a proof-of-concept, we created an R shiny app from ORKG annotations for the Hi Knowledge dataset on 10 major hypotheses in invasion biology (Jeschke & Heger, 2018). Explore the webapp here:

[https://maudbernardverdier.shinyapps.io/Hypothesis-evidence-explorer/ Hypothesis evidence explorer]

== Example application: Teaching ecology ==

[https://orkg.org/list/R674168/ ORKG list - Class assignment: annotating papers in invasion biology]

Sites:WWW/Tools/Classification scheme/page

2024-07-18T05:09:21Z

JonathanJeschke:

Combining expert knowledge with literature analysis, we identified five major research themes in invasion science: (1) introduction pathways, (2) invasion success and invasibility, (3) impacts of invasion, (4) managing biological invasions and (5) meta-invasion science. We divided these themes into ten broader research questions and linked them to 39 major hypotheses forming the theoretical foundation of invasion science (Musseau et al., submitted).

You can explore this conceptual classification scheme of invasion science here:

[https://maudbernardverdier.shinyapps.io/Classification-scheme-invasion-science/]https://maudbernardverdier.shinyapps.io/Classification-scheme-invasion-science/

Sites:WWW/Tools/INBIO/page

2024-07-18T05:06:45Z

JonathanJeschke:

The Invasion Biology Ontology (INBIO) developed in the INAS project ([http://www.doi.org/10.5281/zenodo.6826848 Algergawy et al. 2022]) is an ontology for our [https://hi-knowledge.org/invasion-biology/ initial invasion hypothesis network], which summarises the results of the book “Invasion biology: Hypotheses and evidence” ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). An ontology can be thought of as a machine-readable encyclopaedia, containing the terms and concepts relevant for a specific field, plus their definitions and connections. The aim of INBIO’s first version was to cover those terms and concepts that are relevant in the context of ten major hypotheses in invasion biology included in the small hypothesis network ([https://preprints2020eswc-conferencesorg/posters_demos/paper_279pdf Algergawy et al. 2020]). To create it, we used expert opinion to identify core terms in each of the ten hypotheses. For the Biotic Resistance Hypothesis, as an example, these terms were “''ecosystem''”, “''biodiversity''” and “''species''”. Next, we searched for existing ontologies containing these terms; where this was successful, we used a fusion/merge strategy to integrate respective modules into the INBIO ([https://preprints2020eswc-conferencesorg/posters_demos/paper_279pdf Algergawy et al. 2020]). In further steps, more concepts were added with the aim to provide full conceptual models of the subjects and objects of the ten hypotheses. We plan to expand the INBIO, so that a future version will cover a larger part of the field of invasion biology.

Sites:WWW/Tools/Hypothesis networks/page

2024-07-18T04:59:21Z

JonathanJeschke: /* Invasion biology meets urban ecology: combined hypothesis network */

Hypothesis networks map major hypotheses. They structure and provide an overview of existing theory. Through the hierarchy-of-hypotheses approach ([https://doi.org/10.3897/neobiota.14.3435 Jeschke et al. 2012], [https://doi.org/10.1007/s13280-012-0379-x Heger et al. 2013], [https://doi.org/10.1093/biosci/biaa130 Heger et al. 2021]), hypothesis networks can be hierarchically structured and connected to empirical studies and data. Thus far, we have created several hypothesis networks, two of them are available as hierarchical interactive networks that can be interactively explored (other hypothesis networks in invasion biology, which were created by other methods, are available in [https://doi.org/10.1002/ecs2.2146 Enders et al. 2018] and [https://doi.org/10.3897/neobiota.47.32608 Enders et al. 2019]):


== Invasion biology: large hypothesis network ==

[[File:Invasion biology large hypothesis network.png|center|thumb|600x600px|link=https://hi-knowledge.org/invasion-biology-large/]]

[https://hi-knowledge.org/invasion-biology-large/ Interactive, hierarchically structured network] showing clusters of 39 invasion hypotheses, based on [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] and the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). The hierarchical structure was achieved by applying the hierarchy-of-hypotheses approach. This tool is an extension of the smaller network with 12 hypotheses.



== Invasion biology: hypothesis network book ==

[[File:Invasion biology hypothesis network book.png|center|thumb|600x600px|link=https://hi-knowledge.org/invasion-biology/]]

An [https://hi-knowledge.org/invasion-biology/ interactive visualisation tool] that structures scientific evidence from ca. 1100 publications in a hierarchical network of 12 invasion hypotheses, based on the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]).

== Urban ecology: bipartite hypothesis network ==

[[File:Bipartite Hypothesis Network for Urban Ecology.webp|alt=Bipartite Hypothesis Network for Urban Ecology|center|thumb|600x600px|link=https://doi.org/10.1111/brv.12964]]

Bipartite network of hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)], which are also available in a [https://www.wikidata.org/wiki/Wikidata:WikiProject_Ecology/Task_Force_Urban_Ecology Wikiproject].

== Invasion biology meets urban ecology: combined hypothesis network ==

[[File:Combined urban and invasion hypothesis networks.webp|alt=Forced directed graph of categories and hypotheses in urban and invasion biology|center|thumb|600x600px|link=https://rpubs.com/maudbv/urban-invasion-network]]

[https://rpubs.com/maudbv/urban-invasion-network Interactive visualisation of a combined hypothesis network covering both invasion biology and urban ecology] (cf. [https://doi.org/10.3897/rio.9.e115395 Bernard-Verdier et al. 2023]). This network combines hypotheses in invasion biology from [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] with hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)].

Sites:WWW/Tools/Hypothesis networks/page

2024-07-18T04:58:28Z

JonathanJeschke: /* Invasion biology: hypothesis network book */

Hypothesis networks map major hypotheses. They structure and provide an overview of existing theory. Through the hierarchy-of-hypotheses approach ([https://doi.org/10.3897/neobiota.14.3435 Jeschke et al. 2012], [https://doi.org/10.1007/s13280-012-0379-x Heger et al. 2013], [https://doi.org/10.1093/biosci/biaa130 Heger et al. 2021]), hypothesis networks can be hierarchically structured and connected to empirical studies and data. Thus far, we have created several hypothesis networks, two of them are available as hierarchical interactive networks that can be interactively explored (other hypothesis networks in invasion biology, which were created by other methods, are available in [https://doi.org/10.1002/ecs2.2146 Enders et al. 2018] and [https://doi.org/10.3897/neobiota.47.32608 Enders et al. 2019]):


== Invasion biology: large hypothesis network ==

[[File:Invasion biology large hypothesis network.png|center|thumb|600x600px|link=https://hi-knowledge.org/invasion-biology-large/]]

[https://hi-knowledge.org/invasion-biology-large/ Interactive, hierarchically structured network] showing clusters of 39 invasion hypotheses, based on [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] and the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). The hierarchical structure was achieved by applying the hierarchy-of-hypotheses approach. This tool is an extension of the smaller network with 12 hypotheses.



== Invasion biology: hypothesis network book ==

[[File:Invasion biology hypothesis network book.png|center|thumb|600x600px|link=https://hi-knowledge.org/invasion-biology/]]

An [https://hi-knowledge.org/invasion-biology/ interactive visualisation tool] that structures scientific evidence from ca. 1100 publications in a hierarchical network of 12 invasion hypotheses, based on the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]).

== Urban ecology: bipartite hypothesis network ==

[[File:Bipartite Hypothesis Network for Urban Ecology.webp|alt=Bipartite Hypothesis Network for Urban Ecology|center|thumb|600x600px|link=https://doi.org/10.1111/brv.12964]]

Bipartite network of hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)], which are also available in a [https://www.wikidata.org/wiki/Wikidata:WikiProject_Ecology/Task_Force_Urban_Ecology Wikiproject].

== Invasion biology meets urban ecology: combined hypothesis network ==

[[File:Combined urban and invasion hypothesis networks.webp|alt=Forced directed graph of categories and hypotheses in urban and invasion biology|center|thumb|600x600px|link=https://rpubs.com/maudbv/urban-invasion-network]]

Interactive visualisation of a combined hypothesis network covering both invasion biology and urban ecology (cf. [https://doi.org/10.3897/rio.9.e115395 Bernard-Verdier et al. 2023]). This network combines hypotheses in invasion biology from [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] with hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)].

Sites:WWW/Tools/Hypothesis networks/page

2024-07-18T04:57:44Z

JonathanJeschke: /* Invasion biology: large hypothesis network */

Hypothesis networks map major hypotheses. They structure and provide an overview of existing theory. Through the hierarchy-of-hypotheses approach ([https://doi.org/10.3897/neobiota.14.3435 Jeschke et al. 2012], [https://doi.org/10.1007/s13280-012-0379-x Heger et al. 2013], [https://doi.org/10.1093/biosci/biaa130 Heger et al. 2021]), hypothesis networks can be hierarchically structured and connected to empirical studies and data. Thus far, we have created several hypothesis networks, two of them are available as hierarchical interactive networks that can be interactively explored (other hypothesis networks in invasion biology, which were created by other methods, are available in [https://doi.org/10.1002/ecs2.2146 Enders et al. 2018] and [https://doi.org/10.3897/neobiota.47.32608 Enders et al. 2019]):


== Invasion biology: large hypothesis network ==

[[File:Invasion biology large hypothesis network.png|center|thumb|600x600px|link=https://hi-knowledge.org/invasion-biology-large/]]

[https://hi-knowledge.org/invasion-biology-large/ Interactive, hierarchically structured network] showing clusters of 39 invasion hypotheses, based on [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] and the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). The hierarchical structure was achieved by applying the hierarchy-of-hypotheses approach. This tool is an extension of the smaller network with 12 hypotheses.



== Invasion biology: hypothesis network book ==

[[File:Invasion biology hypothesis network book.png|center|thumb|600x600px|link=https://hi-knowledge.org/invasion-biology/]]

An interactive visualisation tool that structures scientific evidence from ca. 1100 publications in a hierarchical network of 12 invasion hypotheses, based on the book Invasion Biology: Hypotheses and Evidence ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]).

== Urban ecology: bipartite hypothesis network ==

[[File:Bipartite Hypothesis Network for Urban Ecology.webp|alt=Bipartite Hypothesis Network for Urban Ecology|center|thumb|600x600px|link=https://doi.org/10.1111/brv.12964]]

Bipartite network of hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)], which are also available in a [https://www.wikidata.org/wiki/Wikidata:WikiProject_Ecology/Task_Force_Urban_Ecology Wikiproject].

== Invasion biology meets urban ecology: combined hypothesis network ==

[[File:Combined urban and invasion hypothesis networks.webp|alt=Forced directed graph of categories and hypotheses in urban and invasion biology|center|thumb|600x600px|link=https://rpubs.com/maudbv/urban-invasion-network]]

Interactive visualisation of a combined hypothesis network covering both invasion biology and urban ecology (cf. [https://doi.org/10.3897/rio.9.e115395 Bernard-Verdier et al. 2023]). This network combines hypotheses in invasion biology from [https://doi.org/10.1111/geb.13082 Enders et al. (2020)] with hypotheses in urban ecology from [https://doi.org/10.1111/brv.12964 Lokatis et al. (2023)].

Sites:WWW/Tools/Classification scheme/page

2024-07-08T07:17:55Z

JonathanJeschke:

Combining expert knowledge with literature analysis, we identified five major research themes in invasion science: (1) introduction pathways, (2) invasion success and invasibility, (3) impacts of invasion, (4) managing biological invasions and (5) meta-invasion science. We divided these themes into ten broader research questions and linked them to 39 major hypotheses forming the theoretical foundation of invasion science (Musseau et al., submitted). You can explore this conceptual classification scheme of invasion science here:

[https://maudbernardverdier.shinyapps.io/Classification-scheme-invasion-science/]https://maudbernardverdier.shinyapps.io/Classification-scheme-invasion-science/

Sites:WWW/Tools/Wikidata/popup

2024-07-03T14:48:38Z

JonathanJeschke: Created page with "WikiProject Invasion Biology within Wikidata"

WikiProject Invasion Biology within Wikidata

Sites:WWW/Tools/Invasion biology corpus/page

2024-06-27T08:50:07Z

JonathanJeschke: Created page with "Collection of entities related to biological invasions included in Wikidata. The main entity classes in the corpus are taxa with non-native populations, publications related to biological invasions, authors of multiple invasion biology publications, and hypotheses related to invasion biology. The corpus is continuously updated in Wikidata, and a snapshot from mid-2024 is available in Zenodo: [https://zenodo.org/doi/10.5281/zenodo.12518037 https://zenodo.org/doi/10.5281..."

Collection of entities related to biological invasions included in Wikidata. The main entity classes in the corpus are taxa with non-native populations, publications related to biological invasions, authors of multiple invasion biology publications, and hypotheses related to invasion biology.

The corpus is continuously updated in Wikidata, and a snapshot from mid-2024 is available in Zenodo:

[https://zenodo.org/doi/10.5281/zenodo.12518037 https://zenodo.org/doi/10.5281/zenodo.12518037]

Sites:WWW/Tools/On-demand analyses/page

2024-06-27T08:45:18Z

JonathanJeschke:

== About ==

On-demand analyses and visualisations, such as web apps and dashboards, are essential to keep track of the rapidly accumulating data in ecological databases. Such interactive and visual syntheses are a great way to communicate current ecological knowledge to a broad audience (scientists, managers, policy makers, citizens, etc.). Such interactive platforms are designed to target specific fields or questions, for instance evidence in invasion biology theory, current state of biodiversity trends or evidence-based restoration methods.

== Example: Hypothesis evidence explorer ==

We created an R shiny app providing an interactive synthesis of the Hi Knowledge dataset for 10 major hypotheses in invasion biology ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). The app synthesizes standardised information annotated in ORKG (internal link) for each paper about taxa, habitats, methods, continents, and whether or not the study supports one of 10 major hypotheses in invasion biology.

Explore the web app: [https://maudbernardverdier.shinyapps.io/Hypothesis-evidence-explorer/ Hypothesis evidence explorer].

Sites:WWW/Tools/Hypothesis papers/page

2024-06-27T08:44:20Z

JonathanJeschke:

Hypotheses play a central role in the scientific process, yet the way they are introduced often leaves much room for interpretation, which makes it difficult to use them later on: to study and test them, to delineate their scope and to explore the relationships they have to other hypotheses or concepts, to datasets, methodologies or other resources. In [https://riojournal.com/article/119805/ Mietchen et al. (2024)], we introduce a new article type that is dedicated to them: Hypothesis Descriptions. Such articles combine a specific verbal definition of a hypothesis with a concise description of its components and provide pointers to prior work as well as alignments with formal ways of knowledge representation, optionally including relevant nanopublications. With this format, we aim to facilitate the study of hypotheses in and of themselves, to improve their testability along with the documentation and interpretability of such tests, and to stimulate efforts towards standardisation and automation in this space. [https://riojournal.com/article/107393/list/22/ Heger et al. (2024a)] provide an example for the Enemy Release Hypothesis in invasion biology. A generic template for similar publications, applicable also to other research fields and different publication outlets, can be found in [https://riojournal.com/article/119808/ Heger et al. (2024b)].

Sites:WWW/Tools/Causal networks/popup

2024-06-27T08:28:24Z

JonathanJeschke: Created page with "Causal network graphs showing hypothesised mechanisms underlying biological invasions"

Causal network graphs showing hypothesised mechanisms underlying biological invasions

Sites:WWW/Tools/Branches of Science/popup

2024-06-27T08:27:48Z

JonathanJeschke: Created page with "Interactive tool to dive into the different branches of science, as included in Wikipedia, and to find out where you can study them in Germany (from the DAAD database)"

Interactive tool to dive into the different branches of science, as included in Wikipedia, and to find out where you can study them in Germany (from the DAAD database)

Sites:WWW/Tools/INBIO/popup

2024-06-27T08:27:07Z

JonathanJeschke: Created page with "Invasion Biology Ontology: a machine-readable encyclopaedia containing core concepts in invasion biology"

Invasion Biology Ontology: a machine-readable encyclopaedia containing core concepts in invasion biology

Sites:WWW/Tools/INBIO TST/popup

2024-06-27T08:26:31Z

JonathanJeschke: Created page with "Tool for students to explore the field of invasion biology"

Tool for students to explore the field of invasion biology

Sites:WWW/Tools/Invasion biology corpus/popup

2024-06-27T08:23:42Z

JonathanJeschke: Created page with "Collection of publications and other entities related to biological invasions"

Collection of publications and other entities related to biological invasions

Sites:WWW/Tools/Classification scheme/popup

2024-06-27T08:23:04Z

JonathanJeschke: Created page with "Conceptual classification scheme of invasion science that allows to organise publications and datasets, guide research directions and identify knowledge gaps"

Conceptual classification scheme of invasion science that allows to organise publications and datasets, guide research directions and identify knowledge gaps

Sites:WWW/Tools/Hypothesis networks/popup

2024-06-27T08:21:04Z

JonathanJeschke: Created page with "Conceptual maps showing major research hypotheses and how they are related to each other"

Conceptual maps showing major research hypotheses and how they are related to each other

Sites:WWW/Tools/On-demand analyses/popup

2024-06-27T08:20:21Z

JonathanJeschke: Created page with "Online tools providing interactive on-demand analyses and visualisations, e.g. R shiny apps"

Online tools providing interactive on-demand analyses and visualisations, e.g. R shiny apps

Sites:WWW/Tools/Hypothesis papers/popup

2024-06-27T08:19:41Z

JonathanJeschke: Created page with "Standardised articles summarising the definition and history of a scientific hypothesis"

Standardised articles summarising the definition and history of a scientific hypothesis

Sites:WWW/Tools/Nanopublications/popup

2024-06-27T08:19:03Z

JonathanJeschke: Created page with "Nanopublications allow to express individual scientific claims in a way that facilitates their processing by automated workflows"

Nanopublications allow to express individual scientific claims in a way that facilitates their processing by automated workflows

Sites:WWW/Tools/Scholia/popup

2024-06-27T08:18:21Z

JonathanJeschke: Created page with "Visual scholarly profiles based on bibliographic and other information in Wikidata"

Visual scholarly profiles based on bibliographic and other information in Wikidata

Sites:WWW/Tools/OKMaps/popup

2024-06-27T08:17:42Z

JonathanJeschke: Created page with "Query the literature to create knowledge maps and streamgraphs of publications in invasion biology"

Query the literature to create knowledge maps and streamgraphs of publications in invasion biology

Sites:WWW/Tools/ORKG/popup

2024-06-27T08:16:56Z

JonathanJeschke: Created page with "Community-curated platform describing research papers in a structured manner using semantic annotations"

Community-curated platform describing research papers in a structured manner using semantic annotations

Sites:WWW/Tools/Nanopublications/page

2024-06-24T08:15:47Z

JonathanJeschke:

Nanopublications allow to express individual scientific claims in a way that facilitates their processing by automated workflows ([https://nanopub.net https://nanopub.net]). We have, for example, published a set of nanopublications describing invasion hypothesis statements alongside with a hypothesis description paper on the enemy release hypothesis ([https://doi.org/10.3897/rio.10.e107393 Heger et al. 2024]; see list below).
{| class="wikitable"
|'''Nanopublication'''
|'''Creator'''
|'''Date'''
|-
|[http://rio.kpxl.org/RAi4qmpnVXPT0F8ZED_n5LfRMb-rewz5AMS0Ui82QU5N4 reduced pressure by enemies in the non-native range contributes to invasion success]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|27-07-2023 09:08:53
|-
|[http://rio.kpxl.org/RAvk92idktxKQP5jw4fS4Z1RHLz25qO1wY89xLPluozV8 reduced per capita effect of enemies on species in the non-native range increases population-level performance of non-native species]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|11-01-2024 15:40:36
|-
|[http://rio.kpxl.org/RANh-JvcqEfNtczMNqafqvdrwVBFz0AyFM4YOAi9DOKzo changed richness and abundance of enemies in the non-native range increases population-level performance of non-native species]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|11-01-2024 16:03:18
|-
|[http://rio.kpxl.org/RAz-mhk4nvDT6LpytlI66xZbyNn5dDu-n5p2asiPqHabo adaptation in response to enemy release in the non-native range increases population-level performance of non-native species]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|11-01-2024 16:08:27
|-
|[http://rio.kpxl.org/RAj3R1PhqaKbZaHVtEEH_RUoESVS8kzKXRLTCLCSYQNE8 transport to non-native range decreases number of enemies]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 08:53:49
|-
|[http://rio.kpxl.org/RAjqMrFC3phwV01qWR0Uz4lA4RvRUf68zKBc9RueSyM5A reduced pressure by generalist enemies in the non-native range contributes to invasion success]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 08:58:08
|-
|[http://rio.kpxl.org/RAnq454ZDhdzll1bQ2vMfXTTS07fxBee69o1j5u5pc2zs reduced pressure by specialist enemies in the non-native range contributes to invasion success]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 09:04:12
|-
|[http://rio.kpxl.org/RA8TWQp9MJkDfCiI-Ffto96zHuGjmUZi4sWvS3U6Harys number of enemies of invasive species has smaller value than number of enemies of native species]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 09:16:40
|-
|[http://rio.kpxl.org/RA79vwGn_Jf10F3Nv_ITSDq-1bAmShco1x3dN54dCLRTU number of enemies of invasive species in its non-native range has smaller value than number of enemies of invasive species in its native range]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 09:24:33
|-
|[http://rio.kpxl.org/RAYfo5rEg_nYTAGXWWC3wlS_ypsKa5VUhZIX6NciKnlSo reduced pressure by enemies in the non-native range increases performance of non-native species]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 09:28:36
|-
|[http://rio.kpxl.org/RAV8XhVQGWC8E25THzCIboS5PVwPq0A9fWNoLVvRg3a0A absence of enemies in the non-native range contributes to invasion success]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|18-01-2024 09:35:01
|-
|[http://rio.kpxl.org/RAH0b27BDPmQqpasBuRyEnC3_SzrWdWgrimjsRYKMvbm4 reduced pressure by enemies in the non-native range]
|[https://orcid.org/0000-0001-9488-1870 Daniel Mietchen]
|30-05-2023 09:25:02
|}

Sites:WWW/Projects/Early Projects/description

2024-06-24T08:00:49Z

JonathanJeschke:

There were several early projects starting our work on what has later become the Hi Knowledge initiative. In March 2010, we organised the workshop “Tackling the emerging crisis of invasion biology: How can ecological theory, experiments, and field studies be combined to achieve major progress?” in Benediktbeuern, Germany, in the context of the specialist group “Theory in Ecology” of the Ecological Society of Germany, Austria and Switzerland (GfÖ; see [https://doi.org/10.1007/s13280-012-0379-x Heger et al. 2013]). The idea of the hierarchy-of-hypotheses (HoH) approach emerged from fruitful discussions during this workshop and our parallel work on the study “Support for major hypotheses in invasion biology is uneven and declining” ([https://doi.org/10.3897/neobiota.14.3435 Jeschke et al. 2012]), with the main funder Deutsche Forschungsgemeinschaft (DFG) as part of the project “Combining bottom-up and top-down analyses to test fundamental concepts in invasion biology”.

A DFG Heisenberg grant from from 2014 to 2019 allowed us to develop and apply network analysis and web-based approaches to synthesise hypotheses and data in invasion biology and related disciplines. During this time period, we worked on the book “Invasion Biology: Hypotheses and Evidence” ([https://doi.org/10.1079/9781780647647.0000 Jeschke & Heger 2018]). We thought it would be cool to have an interactive website complementing the book, and we decided to call this website “Hi Knowledge”. In parallel, we worked on “Dark Knowledge” ([https://doi.org/10.1139/facets-2019-0007 Jeschke et al. 2019]), and Martin Enders had started his doctoral thesis “Creating and evaluating hypothesis networks in invasion biology” funded by the Foundation of German Business (sdw) and the BMBF in the context of the project Bridging in Biodiversity Science. Martin Enders and collaborators explored and evaluated different approaches to create hypothesis networks, using invasion biology as an example. Two of these hypothesis networks can be interactively explored in our Hi Knowledge website: (i) [https://doi.org/10.1079/9781780647647.0049 Enders & Jeschke (2018)], which was published in the first version of the Hi Knowledge website to complement the above-mentioned book, and (ii) [https://doi.org/10.1111/geb.13082 Enders et al. (2020)].

In 2017 and 2018, we organised a series of three symposia in Hanover, Germany, funded by the VolkswagenStiftung with a focus on the HoH approach. We had inspiring discussions in these symposia with researchers from different fields as well as artists and designers. Several ideas emerged from these discussions, which also allowed us to further improve the HoH approach ([https://doi.org/10.1093/biosci/biaa130 Heger et al. 2021]).