{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T13:30:12Z","timestamp":1773495012468,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2017,12,18]],"date-time":"2017-12-18T00:00:00Z","timestamp":1513555200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Gap-filling is a necessary step to produce quality genome-scale metabolic reconstructions capable of flux-balance simulation. Most available gap-filling tools use an organism-agnostic approach, where reactions are selected from a database to fill gaps without consideration of the target organism. Conversely, our likelihood based gap-filling with probabilistic annotations selects candidate reactions based on a likelihood score derived specifically from the target organism\u2019s genome. Here, we present two new implementations of probabilistic annotation and likelihood based gap-filling: a web service called ProbAnnoWeb, and a standalone python package called ProbAnnoPy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Our tools are available as a web service with no installation needed (ProbAnnoWeb) at probannoweb.systemsbiology.net, and as a local python package implementation (ProbAnnoPy) at github.com\/PriceLab\/probannopy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx796","type":"journal-article","created":{"date-parts":[[2017,12,15]],"date-time":"2017-12-15T17:44:33Z","timestamp":1513359873000},"page":"1594-1596","source":"Crossref","is-referenced-by-count":11,"title":["ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions"],"prefix":"10.1093","volume":"34","author":[{"given":"Brendan","family":"King","sequence":"first","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry","family":"Farrah","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew A","family":"Richards","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Mundy","sequence":"additional","affiliation":[{"name":"Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evangelos","family":"Simeonidis","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan D","family":"Price","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,12,18]]},"reference":[{"key":"2023012713031816000_btx796-B1","doi-asserted-by":"crossref","first-page":"e1003882","DOI":"10.1371\/journal.pcbi.1003882","article-title":"Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models","volume":"10","author":"Benedict","year":"2014","journal-title":"PLoS Comput. 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