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"published": "2023-10-03", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "issn-l": "2046-1402"}, "abstract": "Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.", "doi": "10.12688/f1000research.74502.2", "pmid": "37842337", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10568213"}, {"db": "pii", "key": "ELIXIR-1129"}], "notes": [], "created": "2026-08-20T12:41:46.796Z", "modified": "2026-08-20T12:41:46.982Z"}, {"entity": "publication", "iuid": "b6a320409e2149cdbfdc1dfdc315fa17", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b6a320409e2149cdbfdc1dfdc315fa17.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b6a320409e2149cdbfdc1dfdc315fa17"}}, "title": "ELIXIR and Toxicology: a community in development", "authors": [{"family": "Martens", "given": "Marvin", "initials": "M", "orcid": "0000-0003-2230-0840", "researcher": {"href": 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"given": "Pavel", "initials": "P"}, {"family": "Berka", "given": "Karel", "initials": "K"}, {"family": "Bessems", "given": "Jos", "initials": "J", "orcid": "0000-0001-5718-0733", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06e6aa82d5743c98133c48628244130.json"}}, {"family": "Blaha", "given": "Ludek", "initials": "L"}, {"family": "Bolton", "given": "Evan E", "initials": "EE", "orcid": "0000-0002-5959-6190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43ba499c6c8a44088a25759c10463de9.json"}}, {"family": "Cases", "given": "Montserrat", "initials": "M"}, {"family": "Damalas", "given": "Dimitrios \u0395", "initials": "D\u0395", "orcid": "0000-0002-2997-7566", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa5d565f99f0450b9e209c8b4949bc44.json"}}, {"family": "Dave", "given": "Kirtan", "initials": "K"}, {"family": "Dilger", "given": "Marco", "initials": "M", "orcid": 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"published": "2021-11-08", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "1129", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.74502.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:41:44.020Z", "modified": "2026-08-20T12:41:44.651Z"}, {"entity": "publication", "iuid": "584464f08c2d489fac24dd7feadccfec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/584464f08c2d489fac24dd7feadccfec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/584464f08c2d489fac24dd7feadccfec"}}, "title": "Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud", "authors": [{"family": "Moreno", "given": "Pablo", "initials": "P", "orcid": "0000-0002-9856-1679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db6c8d3acd914554adf19cb900cadba3.json"}}, {"family": "Pireddu", "given": "Luca", 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"2018-12-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/488643", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:46.924Z", "modified": "2026-08-20T11:11:47.550Z"}, {"entity": "publication", "iuid": "ea525cca041145b7bdfe210040715780", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780"}}, "title": "Expanding the Use of Spectral Libraries in Proteomics.", "authors": [{"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": 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Y", "initials": "AY"}, {"family": "Mendoza", "given": "Luis", "initials": "L", "orcid": "0000-0003-0128-8643", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6e8a7feab0f481eaf6acd7ec097c5c5.json"}}, {"family": "Shofstahl", "given": "Jim", "initials": "J"}, {"family": "Dowsey", "given": "Andrew W", "initials": "AW", "orcid": "0000-0002-7404-9128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1cb70e527d84d32b1e995014007efb8.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Salek", "given": "Reza M", "initials": "RM", "orcid": "0000-0001-8604-1732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62799f5748ef484b816827380b723b2c.json"}}, {"family": "Neumann", "given": "Steffen", "initials": "S", "orcid": "0000-0002-7899-7192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fd85c99a6364305ba466010ed3012ec.json"}}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA", "orcid": "0000-0002-0045-7698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f857e16ce82b4242ab0e780c8bec9539.json"}}, {"family": "Lam", "given": "Henry", "initials": "H", "orcid": "0000-0001-7928-0364", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f27cfbc77fe4122977457e89968814c.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N"}, {"family": "R\u00f6st", "given": "Hannes", "initials": "H", "orcid": "0000-0003-0990-7488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4579af772375404da76c447b23c658a3.json"}}], "type": "journal article", "published": "2018-12-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "17", "issue": "12", "pages": "4051-4060", "issn-l": "1535-3893"}, "abstract": "The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.", "doi": "10.1021/acs.jproteome.8b00485", "pmid": "30270626", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1015163"}, {"db": "pmc", "key": "PMC6443480"}], "notes": [], "created": "2026-08-20T08:12:14.655Z", "modified": "2026-08-20T08:12:15.306Z"}]}