{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:38:54Z","timestamp":1761237534644},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"S3","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, \u2018bio-inference,\u2019 as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of \u2018bio-inference\u2019 schemes observed in the pathway corpus.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-s3-s5","type":"journal-article","created":{"date-parts":[[2008,4,11]],"date-time":"2008-04-11T18:14:58Z","timestamp":1207937698000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["New challenges for text mining: mapping between text and manually curated pathways"],"prefix":"10.1186","volume":"9","author":[{"given":"Kanae","family":"Oda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin-Dong","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomoko","family":"Ohta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Okanohara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takuya","family":"Matsuzaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuka","family":"Tateisi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun'ichi","family":"Tsujii","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,4,11]]},"reference":[{"key":"2587_CR1","doi-asserted-by":"publisher","first-page":"D504","DOI":"10.1093\/nar\/gkj126","volume":"34","author":"GD Bader","year":"2006","unstructured":"Bader GD, Cary MP, Sander C: Pathguide: a pathway resource list. 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