SMAFIRA - Artificial Intelligence for Finding Alternative Methods
What is the database about
SMAFIRA is an acronym for SMArt Feature based Interactive RAnking and shall enable scientists to find suitable suggestions for alternative methods to a given animal experiment.
What does the database do?
Although there are already search engines and literature databases for biomedical questions, which also provide semantic techniques, there is still no satisfying solution for the search for alternative methods to animal experiments. So, to support researchers, the Bf3R has developed a search engine for alternative methods to animal experiments that is based on the freely accessible biomedical literature database PubMed (Medline) and that enhances this database with important functions.
SMAFIRA is an acronym for SMArt Feature based Interactive RAnking and shall enable scientists to find suitable suggestions for alternative methods to a given animal experiment (= reference document). Furthermore, SMAFIRA will rank the results of the search, i.e. the reference list with respect to their thematic correspondence to the given reference document and their relevance as a potential alternative method to the respective animal experiment. SMAFIRA incorporates state-of-the-art methods of Natural Language Processing and artificial intelligence.
Background
Before an animal experiment can be conducted as part of a scientific project, it needs to be approved by a competent authority. For this purpose, a researcher has to submit an application for approval in which the fulfillment of scientific and legal requirements is outlined. Part of this application is a thorough literature search to ensure that the planned animal experiment cannot be replaced by an alternative method. Such an alternative would be, for example, a method or procedure that is suitable to answer a specific scientific question without the use of live (vertebrate) animals, e.g., in vitro procedures. The search for possible alternative methods is often very complex and is a major challenge for researchers.
Research
We provide information on the further development of Smafira.
Butzke D, Bert B, Gulich K, Schönfelder G, Neves M. SMAFIRA: a literature-based web tool to assist researchers with retrieval of 3R-relevant information. (2024) Lab Anim. 2024 Aug;58(4):369-373. External Link:https://doi.org/10.1177/00236772241237608
Neves M, Klippert A, Knöspel F, Rudeck J, Stolz A, Ban Z, Becker M, Diederich K, Grune B, Kahnau Pshort forphosphorus, Ohnesorge N, Pucher J, Schönfelder G, Bert B, Butzke D Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments (2023). Journal of Biomedical Semantics:14(13). External Link:https://doi.org/10.1186/s13326-023-00292-w
Neves M. Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods, Genomics & Informatics, 2020, 18(2). External Link:full text and pdf, https://doi.org/10.5808/gi.2020.18.2.e18
Butzke D, Dulisch N, Dunst S, Steinfath M, Neves M, Mathiak B, Grune B. SMAFIRA-c: A benchmark text corpus for evaluation of approaches to relevance ranking and knowledge discovery in the biomedical domain(2020) Research Square. Preprint from Research Square. External Link:full text and pdf, https://doi.org/10.21203/rs.3.rs-16454/v1
Neves M, Butzke D, Grune B. Evaluation of Scientific Elements for Text Similarity in Biomedical Publications(2019) 6th Workshop on Argument Mining,Association for Computer Linguistics. External Link:pdf and bibtex, http://dx.doi.org/10.18653/v1/W19-4515
Neves M, Butzke D, Schönfelder G, Grune B. Bf3R at SemEval-2018 Task 7: Evaluating Two Relation Extraction Tools for Finding Semantic Relations in Biomedical Abstracts (2018), Proceedings of the 12th International Workshop on Semantic Evaluation, Association for Computational Linguistics:816-820. External Link:pdf and bibtex, http://dx.doi.org/10.18653/v1/S18-1130
Neves M, Ševa J. An extensive review of tools for manual annotation of documents, (2019) Briefings in Bioinformatics: 22(1) 146-16External Link: full text, https://doi.org/10.1093/bib/bbz130
Contact
12277 Berlin
Deutschland Postal address: Bundesinstitut für Risikobewertung
Max-Dohrn-Str. 8-10
10589 Berlin
Deutschland Telephone: 030-18412-29001 030-18412-29001 E-mail: bf3r@bfr.bund.de