| 1. |
- Matentzoglu, Nicolas, et al.
(författare)
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A Simple Standard for Ontological Mappings 2023: Updates on data model, collaborations and tooling
- 2023
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Ingår i: Proceedings of the 18th International Workshop on Ontology Matching (OM 2023) co-located with the 22nd International Semantic Web Conference (ISWC 2023). ; , s. 73-78
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Konferensbidrag (refereegranskat)abstract
- The Simple Standard for Ontological Mappings (SSSOM) was first published in December 2021 (v. 0.9). After a number of revisions prompted by community feedback, we have published version 0.15.0 in July 2023. Here we report on the progress made since August 2022, in particular changes to tooling, data model and summary of ongoing standardisation efforts.
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| 2. |
- Moeller, Steffen, et al.
(författare)
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Community-driven development for computational biology at Sprints, Hackathons and Codefests
- 2014
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Ingår i: BMC Bioinformatics. - 1471-2105. ; 15, s. S7-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled unconferences (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.
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| 3. |
- Rubinstein, Yaffa R., et al.
(författare)
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The case for open science : rare diseases
- 2020
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Ingår i: JAMIA Open. - : Oxford University Press (OUP). - 2574-2531. ; 3:3, s. 472-486
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Forskningsöversikt (refereegranskat)abstract
- The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.
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