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| 1 | + |
| 2 | +@article{hinchliff_synthesis_2015, |
| 3 | + title = {Synthesis of phylogeny and taxonomy into a comprehensive tree of life}, |
| 4 | + volume = {112}, |
| 5 | + issn = {0027-8424, 1091-6490}, |
| 6 | + url = {http://www.pnas.org/content/early/2015/09/16/1423041112}, |
| 7 | + doi = {10.1073/pnas.1423041112}, |
| 8 | + abstract = {Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.}, |
| 9 | + language = {en}, |
| 10 | + number = {41}, |
| 11 | + urldate = {2015-09-30}, |
| 12 | + journal = {Proceedings of the National Academy of Sciences}, |
| 13 | + author = {Hinchliff, Cody E. and Smith, Stephen A. and Allman, James F. and Burleigh, J. Gordon and Chaudhary, Ruchi and Coghill, Lyndon M. and Crandall, Keith A. and Deng, Jiabin and Drew, Bryan T. and Gazis, Romina and Gude, Karl and Hibbett, David S. and Katz, Laura A. and Laughinghouse, H. Dail and McTavish, Emily Jane and Midford, Peter E. and Owen, Christopher L. and Ree, Richard H. and Rees, Jonathan A. and Soltis, Douglas E. and Williams, Tiffani and Cranston, Karen A.}, |
| 14 | + month = sep, |
| 15 | + year = {2015}, |
| 16 | + pmid = {26385966}, |
| 17 | + keywords = {biodiversity, Phylogeny, synthesis, Taxonomy, tree of life}, |
| 18 | + pages = {12764--12769}, |
| 19 | + file = {Full Text PDF:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/3EXXWC85/Hinchliff et al. - 2015 - Synthesis of phylogeny and taxonomy into a compreh.pdf:application/pdf;Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/98IFM3X2/1423041112.html:text/html} |
| 20 | +} |
| 21 | + |
| 22 | +@article{redelings_supertree_2017, |
| 23 | + title = {A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species}, |
| 24 | + volume = {5}, |
| 25 | + issn = {2167-8359}, |
| 26 | + url = {https://peerj.com/articles/3058}, |
| 27 | + doi = {10.7717/peerj.3058}, |
| 28 | + abstract = {We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree. We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies. This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project’s “synthetic tree” starting at version 5. This software pipeline is called “propinquity”. It relies heavily on “otcetera”—a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub.}, |
| 29 | + language = {en}, |
| 30 | + urldate = {2017-03-17}, |
| 31 | + journal = {PeerJ}, |
| 32 | + author = {Redelings, Benjamin D. and Holder, Mark T.}, |
| 33 | + month = mar, |
| 34 | + year = {2017}, |
| 35 | + pages = {e3058}, |
| 36 | + file = {Full Text PDF:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/J9TD5XBF/Redelings and Holder - 2017 - A supertree pipeline for summarizing phylogenetic .pdf:application/pdf;Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/MHCI8CSR/3058.html:text/html} |
| 37 | +} |
| 38 | + |
| 39 | +@article{michonneau_rotl:_2016, |
| 40 | + title = {rotl: an {R} package to interact with the {Open} {Tree} of {Life} data}, |
| 41 | + volume = {7}, |
| 42 | + shorttitle = {rotl}, |
| 43 | + url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12593/full}, |
| 44 | + number = {12}, |
| 45 | + journal = {Methods in Ecology and Evolution}, |
| 46 | + author = {Michonneau, François and Brown, Joseph W. and Winter, David J.}, |
| 47 | + year = {2016}, |
| 48 | + pages = {1476--1481}, |
| 49 | + file = {[PDF] peerj.com:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/5ECZPK2B/Michonneau et al. - 2016 - rotl an R package to interact with the Open Tree .pdf:application/pdf;Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/KMEACUG5/full.html:text/html} |
| 50 | +} |
| 51 | + |
| 52 | +@article{mctavish_phylesystem:_2015, |
| 53 | + title = {Phylesystem: a git-based data store for community-curated phylogenetic estimates}, |
| 54 | + volume = {31}, |
| 55 | + issn = {1367-4803}, |
| 56 | + shorttitle = {Phylesystem}, |
| 57 | + url = {https://academic.oup.com/bioinformatics/article/31/17/2794/183373/Phylesystem-a-git-based-data-store-for-community}, |
| 58 | + doi = {10.1093/bioinformatics/btv276}, |
| 59 | + abstract = {Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct.Results: Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git’s version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements.Availability and implementation: Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree.Contact: mtholder@gmail.com}, |
| 60 | + number = {17}, |
| 61 | + urldate = {2017-10-20}, |
| 62 | + journal = {Bioinformatics}, |
| 63 | + author = {McTavish, Emily Jane and Hinchliff, Cody E. and Allman, James F. and Brown, Joseph W. and Cranston, Karen A. and Holder, Mark T. and Rees, Jonathan A. and Smith, Stephen A.}, |
| 64 | + month = sep, |
| 65 | + year = {2015}, |
| 66 | + pages = {2794--2800}, |
| 67 | + file = {Full Text PDF:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/QG8IM5KP/McTavish et al. - 2015 - Phylesystem a git-based data store for community-.pdf:application/pdf;Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/8KM392HQ/btv276.html:text/html} |
| 68 | +} |
| 69 | + |
| 70 | +@article{mctavish_how_2017, |
| 71 | + title = {How and {Why} to {Build} a {Unified} {Tree} of {Life}}, |
| 72 | + volume = {39}, |
| 73 | + issn = {1521-1878}, |
| 74 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201700114}, |
| 75 | + doi = {10.1002/bies.201700114}, |
| 76 | + language = {en}, |
| 77 | + number = {11}, |
| 78 | + urldate = {2018-04-10}, |
| 79 | + journal = {BioEssays}, |
| 80 | + author = {McTavish, Emily Jane and Drew, Bryan T. and Redelings, Ben and Cranston, Karen A.}, |
| 81 | + month = nov, |
| 82 | + year = {2017}, |
| 83 | + file = {Full Text PDF:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/H4QUTY4S/McTavish et al. - 2017 - How and Why to Build a Unified Tree of Life.pdf:application/pdf;Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/I35KQEQC/bies.html:text/html} |
| 84 | +} |
| 85 | + |
| 86 | +@article{rees_automated_2017, |
| 87 | + title = {Automated assembly of a reference taxonomy for phylogenetic data synthesis}, |
| 88 | + issn = {1314-2828}, |
| 89 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515096/}, |
| 90 | + doi = {10.3897/BDJ.5.e12581}, |
| 91 | + number = {5}, |
| 92 | + urldate = {2018-04-10}, |
| 93 | + journal = {Biodiversity Data Journal}, |
| 94 | + author = {Rees, Jonathan A. and Cranston, Karen}, |
| 95 | + month = may, |
| 96 | + year = {2017}, |
| 97 | + pmid = {28765728}, |
| 98 | + pmcid = {PMC5515096}, |
| 99 | + file = {PubMed Central Full Text PDF:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/PIA33BDY/Rees and Cranston - 2017 - Automated assembly of a reference taxonomy for phy.pdf:application/pdf} |
| 100 | +} |
| 101 | + |
| 102 | +@article{sukumaran_dendropy_2010, |
| 103 | + title = {{DendroPy}: a {Python} library for phylogenetic computing}, |
| 104 | + volume = {26}, |
| 105 | + issn = {1367-4803}, |
| 106 | + shorttitle = {{DendroPy}}, |
| 107 | + url = {https://academic.oup.com/bioinformatics/article/26/12/1569/287181}, |
| 108 | + doi = {10.1093/bioinformatics/btq228}, |
| 109 | + abstract = {Abstract. Summary: DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and}, |
| 110 | + language = {en}, |
| 111 | + number = {12}, |
| 112 | + urldate = {2020-07-20}, |
| 113 | + journal = {Bioinformatics}, |
| 114 | + author = {Sukumaran, Jeet and Holder, Mark T.}, |
| 115 | + month = jun, |
| 116 | + year = {2010}, |
| 117 | + note = {Publisher: Oxford Academic}, |
| 118 | + pages = {1569--1571}, |
| 119 | + file = {Full Text PDF:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/IVHQJ9ZY/Sukumaran and Holder - 2010 - DendroPy a Python library for phylogenetic comput.pdf:application/pdf;Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/VDQSUIWZ/287181.html:text/html} |
| 120 | +} |
| 121 | + |
| 122 | +@article{opentreeoflife_open_2019, |
| 123 | + title = {Open {Tree} of {Life} {Synthetic} {Tree}}, |
| 124 | + url = {https://zenodo.org/record/3937742#.XxXISZJKhhH}, |
| 125 | + abstract = {Open Tree of Life aims to construct a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data.}, |
| 126 | + urldate = {2020-07-20}, |
| 127 | + author = {OpenTreeOfLife and Benjamin Redelings and Luna Luisa Sanchez Reyes and Karen A. Cranston and Jim Allman and Mark T. Holder and Emily Jane McTavish}, |
| 128 | + month = dec, |
| 129 | + year = {2019}, |
| 130 | + doi = {10.5281/zenodo.3937742}, |
| 131 | + note = {Publisher: Zenodo}, |
| 132 | + file = {Zenodo Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/63DFWJRH/3937742.html:text/html} |
| 133 | +} |
| 134 | + |
| 135 | +@article{opentreeoflife_open_2019-1, |
| 136 | + title = {Open {Tree} of {Life} {Taxonomy}}, |
| 137 | + url = {https://zenodo.org/record/3937751#.XxXIwJJKhhE}, |
| 138 | + abstract = {The reference taxonomy is an algorithmic combination of several source taxonomies. For code, see the source code repository. Version 3.2 draft 9 was generated using commit 618bab0ca3.}, |
| 139 | + urldate = {2020-07-20}, |
| 140 | + author = {OpenTreeofLife and Karen A. Cranston and Benjamin Redelings and Luna Luisa Sanchez Reyes and Jim Allman and Emily Jane McTavish and Mark T. Holder}, |
| 141 | + month = oct, |
| 142 | + year = {2019}, |
| 143 | + doi = {10.5281/zenodo.3937751}, |
| 144 | + note = {Publisher: Zenodo}, |
| 145 | + file = {Zenodo Snapshot:/home/ejmctavish/.zotero/zotero/n7lb4sp9.default/zotero/storage/V8N696V9/3937751.html:text/html} |
| 146 | +} |
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