Ian Harrow - Academia.edu (original) (raw)
Papers by Ian Harrow
Ontology matching consists of finding correspondences between semantically related entities of tw... more Ontology matching consists of finding correspondences between semantically related entities of two ontologies. OAEI campaigns aim at comparing ontology matching systems on precisely defined test cases. These test cases can use ontologies of different nature (from simple thesauri to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation and consensus. OAEI 2014 offered 7 tracks with 9 test cases followed by 14 participants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentation of the OAEI 2014 campaign. This paper improves on the "Preliminary results" initially published in the on-site proceedings of the ISWC workshop on Ontology Matching (OM-2014). The only official results of the campaign, however, are on the OAEI web site.
HAL (Le Centre pour la Communication Scientifique Directe), Oct 8, 2018
Note that the only official results of the campaign are on the OAEI web site.
CEUR Workshop Proceedings eBooks, Oct 1, 2019
The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems o... more The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2019 campaign offered 11 tracks with 29 test cases, and was attended by 20 participants. This paper is an overall presentation of that campaign.
HAL (Le Centre pour la Communication Scientifique Directe), Oct 8, 2018
Note that the only official results of the campaign are on the OAEI web site.
HAL (Le Centre pour la Communication Scientifique Directe), Oct 18, 2016
Ontology matching consists of finding correspondences between semantically related entities of tw... more Ontology matching consists of finding correspondences between semantically related entities of two ontologies. OAEI campaigns aim at comparing ontology matching systems on precisely defined test cases. These test cases can use ontologies of different nature (from simple thesauri to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation and consensus. OAEI 2014 offered 7 tracks with 9 test cases followed by 14 participants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentation of the OAEI 2014 campaign. This paper improves on the "Preliminary results" initially published in the on-site proceedings of the ISWC workshop on Ontology Matching (OM-2014). The only official results of the campaign, however, are on the OAEI web site.
The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems o... more The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2018 campaign offered 12 tracks with 23 test cases, and was attended by 19 participants. This paper is an overall presentation of that campaign
European Pharmaceutical Review, Jun 1, 2021
This deliverable describes the main objectives and direction of work for the center's dissemi... more This deliverable describes the main objectives and direction of work for the center's dissemination and outreach activities. It presents: brand redesign design and structure of the website selection of social media channels dissemination material such as brochures targeted events such as conferences and workshops communication with industry The document also includes a set of key performance indicators (KPIs) that will be monitored and presented in future reports.
This document is a revised business plan, based upon the previous deliverable that was submitted ... more This document is a revised business plan, based upon the previous deliverable that was submitted 6 months ago. It presents the current stage of findings and has to be viewed as intermediate step towards the final Governance and Business Plan that will be due 18 months from now. The progress that BioExcel has made during the last six months has resulted in a refinement of our strategic development goals. The vision and mission statements have undergone slight adjustments to emphasize BioExcel's focus on biomolecular simulations and modelling, and to highlight the desired impact of enabling better science. While the previous deliverable D5.1 contained a more general description of the HPC ecosystem, we have focused our attention in this revised business plan on our anticipated user base. The value proposition and the description of our support & service offerings have been refined. We acknowledge that we need to focus on where to generate value, and how we are going to do that, in...
This document reports on the dissemination activities of BioExcel for the period until 30 April 2... more This document reports on the dissemination activities of BioExcel for the period until 30 April 2017. Together with D4.5 – Training Report and Updated Plan (PM18), this deliverable gives a complete overview of the work completed under work package 4. The current D4.4 presents information about the project website, social media channels, dissemination events and publications, while D4.5 focuses on the BioExcel Training Programme. Where content overlaps, we specify if a subset of information is presented and refer to the deliverable with the most detailed overview. The project website is one of the main channels for connecting with the wider communities. Its content has substantially increased over the time of the project and it attracts a healthy regular traffic. Social media activities have been successful for promotion. Mailing lists and newsletters have been established for communication with specific interest groups. Webinars have been particularly popular not only for promotion ...
In the BioExcel project, we are establishing a Centre of Excellence (CoE) for<br> Computati... more In the BioExcel project, we are establishing a Centre of Excellence (CoE) for<br> Computational Biomolecular Research. We expect the centre to interact with its users in many ways, and part of our work in the "Consultancy and User Groups" work package is to inform the project about ways in which the centre could usefully work with its users and the wider biomolecular community. This document describes work to date on the evaluation of possible consultancy modalities (that is, ways in which we can offer consultancy) and funding options for these modalities. This document focuses primarily on the former, although it also includes a basic classification of how different modalities could be funded. A second version of this document, due in project month 36, will be more conclusive, and will have a greater emphasis on funding considerations. Core services, for the wider community are likely to be made available free at the point of use, such as services that are accessed ...
BioExcel targets a broad and heterogeneous group of users from the biomolecular research communit... more BioExcel targets a broad and heterogeneous group of users from the biomolecular research community. Different kinds of consultancy and support will work best with different communities. In this project we have explored potential consultancy models through pilot use cases, contributed to a number of proposals for further related activities, and built solid foundations for future professional consultancy by building trust with potential customers. The project ran five Pilot Use Cases (UCs) which had an important role in bringing together work from across the project. The UC <em>Alchemical Free Energy Calculations in Biomolecules </em>covered the field of Free Energy Calculations, in which there is currently strong interest in the wider community, including drug discovery by pharmaceutical companies. It linked GROMACS with pmx, both codes being supported by BioExcel. <em>Molecular Recognition</em>, introduced a test bed where two BioExcel codes (HADDOCK and GROM...
This document follows on from D3.3 "Consultancy Modalities and Funding Options, Half- Time U... more This document follows on from D3.3 "Consultancy Modalities and Funding Options, Half- Time Update". It is intended to be read in conjunction with D3.3, as it does not aim to repeat the content therein. The structure of the documents is similar, to allow cross- referencing. It aims to relate the more theoretical list of modalities presented in D3.3 with specific activities undertaken in the project. BioExcel has used several modalities in activities aimed at the wider community including web pages, a discussion/feedback forum, workflow portals of different types (including software-as-a-service, and those providing access to workflow components), white papers, webinars, face-to-face meetings of various kinds (including Interest Group meetings, workshops, a community forum meeting and multiple face-to-face training courses), online meetings and calls. Fewer of the modalities categorised as being important for professional products and services have been evaluated in BioExcel...
BioExcel has identified and classified a list of communities of interest and from this a set of i... more BioExcel has identified and classified a list of communities of interest and from this a set of initial Interest Groups (IGs) has been selected. This selection is part of an ongoing process of engagement, which is described later in the document. The process of establishing these initial IGs is now underway. The initial IGs are "Biomolecular simulations entry level users", "Integrative modelling", "Free energy calculations", "Hybrid methods for biomolecular systems", "Best practices for performance tuning", and "Practical applications for industry". A key feature of most of these groups is that they can be built from established user-communities of the project's key codes. IGs will be supported with mailing lists, and forums, the latter being provided by the Discourse platform. Additional tools and activities such as blogs and real- time chat will be provided in response to the needs of the groups. Webinars will also fo...
One main objective of BioExcel as a publicly fully funded project is to exploit opportunities for... more One main objective of BioExcel as a publicly fully funded project is to exploit opportunities for commercialization of products and services stemming from its activities, as well as identifying a range of funding schemes for long-term sustainable operations. This deliverable presents the work undertaken to date with respect to inspection of a viable business model based on the experiences from research conducted in the first phase of BioExcel. To avoid repetition, we have not included results and conclusions already presented in previous deliverables (see footnote 1 on page 6). Using the widely adopted Business Model Canvas tool, we analyse the value chain of infrastructure, offerings, customers and financing. Workflows (WF) solutions (generic and custom ones), which package core applications with auxiliary tools for molecular modelling, have been identified as products that are highly needed by the wider communities. They improve the productivity of researchers, allow for efficient...
This document describes the data management strategy for the four BioExcel-2 Use Cases that are a... more This document describes the data management strategy for the four BioExcel-2 Use Cases that are already described in the concurrent deliverable D3.1 - Use Case Work Plans, namely: Use Case 1: Antibody Design<br> Use Case 2: High-throughput Modelling of Interactomes Use Case 3: Rational Drug Design<br> Use Case 4: Electronic Interaction Phenomena The general data management principles and strategy are described, and detailed data management plans are given for data that is expected to be produced as part of the Use Cases. These include how the data will be stored and made findable and accessible, and preserved for future use beyond the lifespan of the current project.
Drug Discovery Today, 2022
Over recent years, there has been exciting growth in collaboration between academia and industry ... more Over recent years, there has been exciting growth in collaboration between academia and industry in the life sciences to make data more Findable, Accessible, Interoperable and Reusable (FAIR) to achieve greater value. Despite considerable progress, the transformative shift from an application-centric to a data-centric perspective, enabled by FAIR implementation, remains very much a work in progress on the 'FAIR journey'. In this review, we consider use cases for FAIR implementation. These can be deployed alongside assessment of data quality to maximize the value of data generated from research, clinical trials, and real-world healthcare data, which are essential for the discovery and development of new medical treatments by biopharma.
This document is the fourth deliverable from WP3 Consultancy and User Groups. The project's s... more This document is the fourth deliverable from WP3 Consultancy and User Groups. The project's structure requires that there is a good flow of feedback between end-users and the many activities spread amongst the project's work packages(WPs). It provides an opportunity to take stock and report on the efficacy of feedback in the project. Overall, feedback in the project is good, but it is important to continue to monitor both external and internal feedback. With the former, we need to broaden the areas in which this occurs beyond the current scope, which is focused on the project's main codes. Internal feedback processes could be more explicit to maintain good feedback as the centre grows. The document considers each work package in turn and depicts graphically the strength of feedback with other parts of the project and with external stakeholders. We look at the current state, a desirable future state, and then consider what could be done to reach the future state. Feedback...
Ontology matching consists of finding correspondences between semantically related entities of tw... more Ontology matching consists of finding correspondences between semantically related entities of two ontologies. OAEI campaigns aim at comparing ontology matching systems on precisely defined test cases. These test cases can use ontologies of different nature (from simple thesauri to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation and consensus. OAEI 2014 offered 7 tracks with 9 test cases followed by 14 participants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentation of the OAEI 2014 campaign. This paper improves on the "Preliminary results" initially published in the on-site proceedings of the ISWC workshop on Ontology Matching (OM-2014). The only official results of the campaign, however, are on the OAEI web site.
HAL (Le Centre pour la Communication Scientifique Directe), Oct 8, 2018
Note that the only official results of the campaign are on the OAEI web site.
CEUR Workshop Proceedings eBooks, Oct 1, 2019
The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems o... more The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2019 campaign offered 11 tracks with 29 test cases, and was attended by 20 participants. This paper is an overall presentation of that campaign.
HAL (Le Centre pour la Communication Scientifique Directe), Oct 8, 2018
Note that the only official results of the campaign are on the OAEI web site.
HAL (Le Centre pour la Communication Scientifique Directe), Oct 18, 2016
Ontology matching consists of finding correspondences between semantically related entities of tw... more Ontology matching consists of finding correspondences between semantically related entities of two ontologies. OAEI campaigns aim at comparing ontology matching systems on precisely defined test cases. These test cases can use ontologies of different nature (from simple thesauri to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation and consensus. OAEI 2014 offered 7 tracks with 9 test cases followed by 14 participants. Since 2010, the campaign has been using a new evaluation modality which provides more automation to the evaluation. This paper is an overall presentation of the OAEI 2014 campaign. This paper improves on the "Preliminary results" initially published in the on-site proceedings of the ISWC workshop on Ontology Matching (OM-2014). The only official results of the campaign, however, are on the OAEI web site.
The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems o... more The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2018 campaign offered 12 tracks with 23 test cases, and was attended by 19 participants. This paper is an overall presentation of that campaign
European Pharmaceutical Review, Jun 1, 2021
This deliverable describes the main objectives and direction of work for the center's dissemi... more This deliverable describes the main objectives and direction of work for the center's dissemination and outreach activities. It presents: brand redesign design and structure of the website selection of social media channels dissemination material such as brochures targeted events such as conferences and workshops communication with industry The document also includes a set of key performance indicators (KPIs) that will be monitored and presented in future reports.
This document is a revised business plan, based upon the previous deliverable that was submitted ... more This document is a revised business plan, based upon the previous deliverable that was submitted 6 months ago. It presents the current stage of findings and has to be viewed as intermediate step towards the final Governance and Business Plan that will be due 18 months from now. The progress that BioExcel has made during the last six months has resulted in a refinement of our strategic development goals. The vision and mission statements have undergone slight adjustments to emphasize BioExcel's focus on biomolecular simulations and modelling, and to highlight the desired impact of enabling better science. While the previous deliverable D5.1 contained a more general description of the HPC ecosystem, we have focused our attention in this revised business plan on our anticipated user base. The value proposition and the description of our support & service offerings have been refined. We acknowledge that we need to focus on where to generate value, and how we are going to do that, in...
This document reports on the dissemination activities of BioExcel for the period until 30 April 2... more This document reports on the dissemination activities of BioExcel for the period until 30 April 2017. Together with D4.5 – Training Report and Updated Plan (PM18), this deliverable gives a complete overview of the work completed under work package 4. The current D4.4 presents information about the project website, social media channels, dissemination events and publications, while D4.5 focuses on the BioExcel Training Programme. Where content overlaps, we specify if a subset of information is presented and refer to the deliverable with the most detailed overview. The project website is one of the main channels for connecting with the wider communities. Its content has substantially increased over the time of the project and it attracts a healthy regular traffic. Social media activities have been successful for promotion. Mailing lists and newsletters have been established for communication with specific interest groups. Webinars have been particularly popular not only for promotion ...
In the BioExcel project, we are establishing a Centre of Excellence (CoE) for<br> Computati... more In the BioExcel project, we are establishing a Centre of Excellence (CoE) for<br> Computational Biomolecular Research. We expect the centre to interact with its users in many ways, and part of our work in the "Consultancy and User Groups" work package is to inform the project about ways in which the centre could usefully work with its users and the wider biomolecular community. This document describes work to date on the evaluation of possible consultancy modalities (that is, ways in which we can offer consultancy) and funding options for these modalities. This document focuses primarily on the former, although it also includes a basic classification of how different modalities could be funded. A second version of this document, due in project month 36, will be more conclusive, and will have a greater emphasis on funding considerations. Core services, for the wider community are likely to be made available free at the point of use, such as services that are accessed ...
BioExcel targets a broad and heterogeneous group of users from the biomolecular research communit... more BioExcel targets a broad and heterogeneous group of users from the biomolecular research community. Different kinds of consultancy and support will work best with different communities. In this project we have explored potential consultancy models through pilot use cases, contributed to a number of proposals for further related activities, and built solid foundations for future professional consultancy by building trust with potential customers. The project ran five Pilot Use Cases (UCs) which had an important role in bringing together work from across the project. The UC <em>Alchemical Free Energy Calculations in Biomolecules </em>covered the field of Free Energy Calculations, in which there is currently strong interest in the wider community, including drug discovery by pharmaceutical companies. It linked GROMACS with pmx, both codes being supported by BioExcel. <em>Molecular Recognition</em>, introduced a test bed where two BioExcel codes (HADDOCK and GROM...
This document follows on from D3.3 "Consultancy Modalities and Funding Options, Half- Time U... more This document follows on from D3.3 "Consultancy Modalities and Funding Options, Half- Time Update". It is intended to be read in conjunction with D3.3, as it does not aim to repeat the content therein. The structure of the documents is similar, to allow cross- referencing. It aims to relate the more theoretical list of modalities presented in D3.3 with specific activities undertaken in the project. BioExcel has used several modalities in activities aimed at the wider community including web pages, a discussion/feedback forum, workflow portals of different types (including software-as-a-service, and those providing access to workflow components), white papers, webinars, face-to-face meetings of various kinds (including Interest Group meetings, workshops, a community forum meeting and multiple face-to-face training courses), online meetings and calls. Fewer of the modalities categorised as being important for professional products and services have been evaluated in BioExcel...
BioExcel has identified and classified a list of communities of interest and from this a set of i... more BioExcel has identified and classified a list of communities of interest and from this a set of initial Interest Groups (IGs) has been selected. This selection is part of an ongoing process of engagement, which is described later in the document. The process of establishing these initial IGs is now underway. The initial IGs are "Biomolecular simulations entry level users", "Integrative modelling", "Free energy calculations", "Hybrid methods for biomolecular systems", "Best practices for performance tuning", and "Practical applications for industry". A key feature of most of these groups is that they can be built from established user-communities of the project's key codes. IGs will be supported with mailing lists, and forums, the latter being provided by the Discourse platform. Additional tools and activities such as blogs and real- time chat will be provided in response to the needs of the groups. Webinars will also fo...
One main objective of BioExcel as a publicly fully funded project is to exploit opportunities for... more One main objective of BioExcel as a publicly fully funded project is to exploit opportunities for commercialization of products and services stemming from its activities, as well as identifying a range of funding schemes for long-term sustainable operations. This deliverable presents the work undertaken to date with respect to inspection of a viable business model based on the experiences from research conducted in the first phase of BioExcel. To avoid repetition, we have not included results and conclusions already presented in previous deliverables (see footnote 1 on page 6). Using the widely adopted Business Model Canvas tool, we analyse the value chain of infrastructure, offerings, customers and financing. Workflows (WF) solutions (generic and custom ones), which package core applications with auxiliary tools for molecular modelling, have been identified as products that are highly needed by the wider communities. They improve the productivity of researchers, allow for efficient...
This document describes the data management strategy for the four BioExcel-2 Use Cases that are a... more This document describes the data management strategy for the four BioExcel-2 Use Cases that are already described in the concurrent deliverable D3.1 - Use Case Work Plans, namely: Use Case 1: Antibody Design<br> Use Case 2: High-throughput Modelling of Interactomes Use Case 3: Rational Drug Design<br> Use Case 4: Electronic Interaction Phenomena The general data management principles and strategy are described, and detailed data management plans are given for data that is expected to be produced as part of the Use Cases. These include how the data will be stored and made findable and accessible, and preserved for future use beyond the lifespan of the current project.
Drug Discovery Today, 2022
Over recent years, there has been exciting growth in collaboration between academia and industry ... more Over recent years, there has been exciting growth in collaboration between academia and industry in the life sciences to make data more Findable, Accessible, Interoperable and Reusable (FAIR) to achieve greater value. Despite considerable progress, the transformative shift from an application-centric to a data-centric perspective, enabled by FAIR implementation, remains very much a work in progress on the 'FAIR journey'. In this review, we consider use cases for FAIR implementation. These can be deployed alongside assessment of data quality to maximize the value of data generated from research, clinical trials, and real-world healthcare data, which are essential for the discovery and development of new medical treatments by biopharma.
This document is the fourth deliverable from WP3 Consultancy and User Groups. The project's s... more This document is the fourth deliverable from WP3 Consultancy and User Groups. The project's structure requires that there is a good flow of feedback between end-users and the many activities spread amongst the project's work packages(WPs). It provides an opportunity to take stock and report on the efficacy of feedback in the project. Overall, feedback in the project is good, but it is important to continue to monitor both external and internal feedback. With the former, we need to broaden the areas in which this occurs beyond the current scope, which is focused on the project's main codes. Internal feedback processes could be more explicit to maintain good feedback as the centre grows. The document considers each work package in turn and depicts graphically the strength of feedback with other parts of the project and with external stakeholders. We look at the current state, a desirable future state, and then consider what could be done to reach the future state. Feedback...