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تسجيل مستخدم جديدBuilding a PubMed knowledge graph
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PubMed is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguated, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National Institutes of Health (NIH) ExPORTER, collecting affiliation history and educational background of authors from ORCID, and identifying fine-grained affiliation data from MapAffil. Through the integration of the credible multi-source data, we could create connections among the bio-entities, authors, articles, affiliations, and funding. Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation (AND) achieving a F1 score of 98.09%. PKG can trigger broader innovations, not only enabling us to measure scholarly impact, knowledge usage, and knowledge transfer, but also assisting us in profiling authors and organizations based on their connections with bio-entities. The PKG is freely available on Figshare (https://figshare.com/s/6327a55355fc2c99f3a2, simplified version that exclude PubMed raw data) and TACC website (http://er.tacc.utexas.edu/datasets/ped, full version).
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Due to the lack of structure, scholarly knowledge remains hardly accessible for machines. Scholarly knowledge graphs have been proposed as a solution. Creating such a knowledge graph requires manual effort and domain experts, and is therefore time-co
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Current science communication has a number of drawbacks and bottlenecks which have been subject of discussion lately: Among others, the rising number of published articles makes it nearly impossible to get a full overview of the state of the art in a
certain field, or reproducibility is hampered by fixed-length, document-based publications which normally cannot cover all details of a research work. Recently, several initiatives have proposed knowledge graphs (KG) for organising scientific information as a solution to many of the current issues. The focus of these proposals is, however, usually restricted to very specific use cases. In this paper, we aim to transcend this limited perspective and present a comprehensive analysis of requirements for an Open Research Knowledge Graph (ORKG) by (a) collecting and reviewing daily core tasks of a scientist, (b) establishing their consequential requirements for a KG-based system, (c) identifying overlaps and specificities, and their coverage in current solutions. As a result, we map necessary and desirable requirements for successful KG-based science communication, derive implications, and outline possible solutions.
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