Skip to content

Commit

Permalink
Merge pull request #6179 from openjournals/joss.07264
Browse files Browse the repository at this point in the history 
Merging automatically
  • Loading branch information
@editorialbot
editorialbot authored Nov 23, 2024
2 parents 8c56836 + 2fa762d commit d69c141
Show file tree
Hide file tree
Showing 4 changed files with 1,083 additions and 0 deletions.
386 changes: 386 additions & 0 deletions joss.07264/10.21105.joss.07264.crossref.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,386 @@
<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1"
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd"
xmlns:rel="http://www.crossref.org/relations.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
version="5.3.1"
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd">
<head>
<doi_batch_id>20241123152458-1c762b3b58da3b2d842c8e223f57ae6efe1dba8a</doi_batch_id>
<timestamp>20241123152458</timestamp>
<depositor>
<depositor_name>JOSS Admin</depositor_name>
<email_address>[email protected]</email_address>
</depositor>
<registrant>The Open Journal</registrant>
</head>
<body>
<journal>
<journal_metadata>
<full_title>Journal of Open Source Software</full_title>
<abbrev_title>JOSS</abbrev_title>
<issn media_type="electronic">2475-9066</issn>
<doi_data>
<doi>10.21105/joss</doi>
<resource>https://joss.theoj.org</resource>
</doi_data>
</journal_metadata>
<journal_issue>
<publication_date media_type="online">
<month>11</month>
<year>2024</year>
</publication_date>
<journal_volume>
<volume>9</volume>
</journal_volume>
<issue>103</issue>
</journal_issue>
<journal_article publication_type="full_text">
<titles>
<title>PhenoFeatureFinder: a python package for linking
developmental phenotypes to omics features</title>
</titles>
<contributors>
<person_name sequence="first" contributor_role="author">
<given_name>Lissy-Anne M.</given_name>
<surname>Denkers</surname>
<affiliations>
<institution><institution_name>University of Amsterdam, Department of Plant Physiology, Green Life Science Research Theme, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands</institution_name></institution>
</affiliations>
<ORCID>https://orcid.org/0009-0004-8222-8689</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Marc D.</given_name>
<surname>Galland</surname>
<affiliations>
<institution><institution_name>INRAE, Institute of Genetics, Environment and Plant Protection (IGEPP—Joint Research Unit 1349), Le Rheu, France</institution_name></institution>
</affiliations>
<ORCID>https://orcid.org/0000-0003-2161-8689</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Annabel</given_name>
<surname>Dekker</surname>
<affiliations>
<institution><institution_name>Enza Zaden R&amp;D B.V., BTR-BM Bioinformatics, Enkhuizen, The Netherlands</institution_name></institution>
</affiliations>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Valerio</given_name>
<surname>Bianchi</surname>
<affiliations>
<institution><institution_name>Enza Zaden R&amp;D B.V., BTR-BM Bioinformatics, Enkhuizen, The Netherlands</institution_name></institution>
<institution><institution_name>Wageningen Bioveterinary Research, Wageningen University &amp; Research, Lelystad, Netherlands</institution_name></institution>
</affiliations>
<ORCID>https://orcid.org/0000-0001-9025-7923</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Petra M.</given_name>
<surname>Bleeker</surname>
<affiliations>
<institution><institution_name>University of Amsterdam, Department of Plant Physiology, Green Life Science Research Theme, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands</institution_name></institution>
</affiliations>
<ORCID>https://orcid.org/0000-0003-2222-9263</ORCID>
</person_name>
</contributors>
<publication_date>
<month>11</month>
<day>23</day>
<year>2024</year>
</publication_date>
<pages>
<first_page>7264</first_page>
</pages>
<publisher_item>
<identifier id_type="doi">10.21105/joss.07264</identifier>
</publisher_item>
<ai:program name="AccessIndicators">
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
</ai:program>
<rel:program>
<rel:related_item>
<rel:description>Software archive</rel:description>
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.14179966</rel:inter_work_relation>
</rel:related_item>
<rel:related_item>
<rel:description>GitHub review issue</rel:description>
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/7264</rel:inter_work_relation>
</rel:related_item>
</rel:program>
<doi_data>
<doi>10.21105/joss.07264</doi>
<resource>https://joss.theoj.org/papers/10.21105/joss.07264</resource>
<collection property="text-mining">
<item>
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.07264.pdf</resource>
</item>
</collection>
</doi_data>
<citation_list>
<citation key="Dalio2021">
<article_title>Contribution of omics and systems biology to
plant biotechnology</article_title>
<author>Dalio</author>
<doi>10.1007/978-3-030-80352-0_10</doi>
<cYear>2021</cYear>
<unstructured_citation>Dalio, R. J. D., Litholdo, C. G.,
Arena, G., Magalhães, D., &amp; Machado, M. A. (2021). Contribution of
omics and systems biology to plant biotechnology (pp. 171–188).
https://doi.org/10.1007/978-3-030-80352-0_10</unstructured_citation>
</citation>
<citation key="Erb2020">
<article_title>Plant secondary metabolites as defenses,
regulators, and primary metabolites: The blurred functional
trichotomy</article_title>
<author>Erb</author>
<journal_title>Plant Physiology</journal_title>
<volume>184</volume>
<doi>10.1104/pp.20.00433</doi>
<issn>0032-0889</issn>
<cYear>2020</cYear>
<unstructured_citation>Erb, M., &amp; Kliebenstein, D. J.
(2020). Plant secondary metabolites as defenses, regulators, and primary
metabolites: The blurred functional trichotomy. Plant Physiology, 184,
39–52. https://doi.org/10.1104/pp.20.00433</unstructured_citation>
</citation>
<citation key="García-Olmedo1998">
<article_title>Plant defense peptides</article_title>
<author>García-Olmedo</author>
<journal_title>Biopolymers</journal_title>
<volume>47</volume>
<doi>10.1002/(SICI)1097-0282(1998)47:6&lt;479::AID-BIP6&gt;3.0.CO;2-K</doi>
<cYear>1998</cYear>
<unstructured_citation>García-Olmedo, F., Molina, A.,
Alamillo, J. M., &amp; Rodríguez-Palenzuéla, P. (1998). Plant defense
peptides. Biopolymers, 47, 479–491.
https://doi.org/10.1002/(SICI)1097-0282(1998)47:6&lt;479::AID-BIP6&gt;3.0.CO;2-K</unstructured_citation>
</citation>
<citation key="Kortbeek2021">
<article_title>Natural variation in wild tomato trichomes;
selecting metabolites that contribute to insect resistance using a
random forest approach</article_title>
<author>Kortbeek</author>
<journal_title>BMC Plant Biology</journal_title>
<volume>21</volume>
<doi>10.1186/s12870-021-03070-x</doi>
<issn>1471-2229</issn>
<cYear>2021</cYear>
<unstructured_citation>Kortbeek, R. W. J., Galland, M. D.,
Muras, A., Kloet, F. M. van der, André, B., Heilijgers, M., Hijum, S. A.
F. T. van, Haring, M. A., Schuurink, R. C., &amp; Bleeker, P. M. (2021).
Natural variation in wild tomato trichomes; selecting metabolites that
contribute to insect resistance using a random forest approach. BMC
Plant Biology, 21, 315.
https://doi.org/10.1186/s12870-021-03070-x</unstructured_citation>
</citation>
<citation key="Lee2020">
<article_title>Persist or perish: Critical life stages
determine the sensitivity of invertebrates to
disturbances</article_title>
<author>Lee</author>
<journal_title>Aquatic Sciences</journal_title>
<volume>82</volume>
<doi>10.1007/s00027-020-0698-0</doi>
<issn>1420-9055</issn>
<cYear>2020</cYear>
<unstructured_citation>Lee, G. H. van der, Kraak, M. H. S.,
Verdonschot, R. C. M., &amp; Verdonschot, P. F. M. (2020). Persist or
perish: Critical life stages determine the sensitivity of invertebrates
to disturbances. Aquatic Sciences, 82.
https://doi.org/10.1007/s00027-020-0698-0</unstructured_citation>
</citation>
<citation key="Liebal2020">
<article_title>Machine learning applications for mass
spectrometry-based metabolomics</article_title>
<author>Liebal</author>
<journal_title>Metabolites</journal_title>
<volume>10</volume>
<doi>10.3390/metabo10060243</doi>
<issn>2218-1989</issn>
<cYear>2020</cYear>
<unstructured_citation>Liebal, U. W., Phan, A. N. T.,
Sudhakar, M., Raman, K., &amp; Blank, L. M. (2020). Machine learning
applications for mass spectrometry-based metabolomics. Metabolites, 10,
243. https://doi.org/10.3390/metabo10060243</unstructured_citation>
</citation>
<citation key="Ma2022">
<article_title>A sublethal concentration of afidopyropen
suppresses the population growth of the cotton aphid, aphis gossypii
glover (hemiptera: aphididae)</article_title>
<author>Ma</author>
<journal_title>Journal of Integrative
Agriculture</journal_title>
<volume>21</volume>
<doi>10.1016/S2095-3119(21)63714-0</doi>
<isbn>8613611281656</isbn>
<cYear>2022</cYear>
<unstructured_citation>Ma, K., Tang, Q., Liang, P., Li, J.,
&amp; Gao, X. (2022). A sublethal concentration of afidopyropen
suppresses the population growth of the cotton aphid, aphis gossypii
glover (hemiptera: aphididae). Journal of Integrative Agriculture, 21,
2055–2064.
https://doi.org/10.1016/S2095-3119(21)63714-0</unstructured_citation>
</citation>
<citation key="Maharijaya2019">
<article_title>Genetic variation in phytochemicals in leaves
of pepper (capsicum) in relation to thrips resistance</article_title>
<author>Maharijaya</author>
<journal_title>Arthropod-Plant Interactions</journal_title>
<volume>13</volume>
<doi>10.1007/s11829-018-9628-7</doi>
<issn>1872-8855</issn>
<isbn>0123456789</isbn>
<cYear>2019</cYear>
<unstructured_citation>Maharijaya, A., Vosman, B., Pelgrom,
K., Wahyuni, Y., Vos, R. C. H. de, &amp; Voorrips, R. E. (2019). Genetic
variation in phytochemicals in leaves of pepper (capsicum) in relation
to thrips resistance. Arthropod-Plant Interactions, 13, 1–9.
https://doi.org/10.1007/s11829-018-9628-7</unstructured_citation>
</citation>
<citation key="Muema2016">
<article_title>Potential of camellia sinensis
proanthocyanidins-rich fraction for controlling malaria mosquito
populations through disruption of larval development</article_title>
<author>Muema</author>
<journal_title>Parasites &amp; Vectors</journal_title>
<volume>9</volume>
<doi>10.1186/s13071-016-1789-6</doi>
<issn>1756-3305</issn>
<cYear>2016</cYear>
<unstructured_citation>Muema, J. M., Bargul, J. L., Nyanjom,
S. G., Mutunga, J. M., &amp; Njeru, S. N. (2016). Potential of camellia
sinensis proanthocyanidins-rich fraction for controlling malaria
mosquito populations through disruption of larval development. Parasites
&amp; Vectors, 9, 512.
https://doi.org/10.1186/s13071-016-1789-6</unstructured_citation>
</citation>
<citation key="Muse2021">
<article_title>On the log-logistic distribution and its
generalizations: A survey</article_title>
<author>Muse</author>
<journal_title>International Journal of Statistics and
Probability</journal_title>
<volume>10</volume>
<doi>10.5539/ijsp.v10n3p93</doi>
<issn>1927-7040</issn>
<cYear>2021</cYear>
<unstructured_citation>Muse, A. H., Mwalili, S. M., &amp;
Ngesa, O. (2021). On the log-logistic distribution and its
generalizations: A survey. International Journal of Statistics and
Probability, 10, 93.
https://doi.org/10.5539/ijsp.v10n3p93</unstructured_citation>
</citation>
<citation key="Olson2016">
<article_title>Evaluation of a tree-based pipeline
optimization tool for automating data science</article_title>
<author>Olson</author>
<journal_title>Proceedings of the Genetic and Evolutionary
Computation Conference 2016</journal_title>
<doi>10.1145/2908812.2908918</doi>
<isbn>9781450342063</isbn>
<cYear>2016</cYear>
<unstructured_citation>Olson, R. S., Bartley, N.,
Urbanowicz, R. J., &amp; Moore, J. H. (2016). Evaluation of a tree-based
pipeline optimization tool for automating data science. Proceedings of
the Genetic and Evolutionary Computation Conference 2016, 485–492.
https://doi.org/10.1145/2908812.2908918</unstructured_citation>
</citation>
<citation key="Pedregosa2011">
<article_title>Scikit-learn: Machine learning in
python</article_title>
<author>Pedregosa</author>
<journal_title>Journal of Machine Learning
Research</journal_title>
<volume>12</volume>
<cYear>2011</cYear>
<unstructured_citation>Pedregosa, F., Varoquaux, G.,
Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M.,
Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A.,
Cournapeau, D., Brucher, M., Perrot, M., &amp; Duchesnay, É. (2011).
Scikit-learn: Machine learning in python. Journal of Machine Learning
Research, 12, 2825–2830.
https://dl.acm.org/doi/10.5555/1953048.2078195</unstructured_citation>
</citation>
<citation key="Ritz2015">
<article_title>Dose-response analysis using
R</article_title>
<author>Ritz</author>
<journal_title>PLoS ONE</journal_title>
<volume>10</volume>
<doi>10.1371/journal.pone.0146021</doi>
<cYear>2015</cYear>
<unstructured_citation>Ritz, C., Baty, F., Streibig, J. C.,
&amp; Gerhard, D. (2015). Dose-response analysis using R. PLoS ONE, 10,
1–13.
https://doi.org/10.1371/journal.pone.0146021</unstructured_citation>
</citation>
<citation key="Seefeldt1995">
<article_title>Log-logistic analysis of herbicide
dose-response relationships</article_title>
<author>Seefeldt</author>
<journal_title>Weed Technology</journal_title>
<volume>9</volume>
<doi>10.1017/s0890037x00023253</doi>
<cYear>1995</cYear>
<unstructured_citation>Seefeldt, S. S., Jensen, J. E., &amp;
Fuerst, E. P. (1995). Log-logistic analysis of herbicide dose-response
relationships. Weed Technology, 9, 218–227.
https://doi.org/10.1017/s0890037x00023253</unstructured_citation>
</citation>
<citation key="Song2021">
<article_title>High-throughput phenotyping: Breaking through
the bottleneck in future crop breeding</article_title>
<author>Song</author>
<journal_title>The Crop Journal</journal_title>
<volume>9</volume>
<doi>10.1016/j.cj.2021.03.015</doi>
<cYear>2021</cYear>
<unstructured_citation>Song, P., Wang, J., Guo, X., Yang,
W., &amp; Zhao, C. (2021). High-throughput phenotyping: Breaking through
the bottleneck in future crop breeding. The Crop Journal, 9, 633–645.
https://doi.org/10.1016/j.cj.2021.03.015</unstructured_citation>
</citation>
<citation key="Vliet2013">
<article_title>Statistics for analyzing ecotoxicity test
data</article_title>
<author>Vliet</author>
<journal_title>Encyclopedia of Aquatic
Ecotoxicology</journal_title>
<doi>10.1007/978-94-007-5704-2</doi>
<cYear>2013</cYear>
<unstructured_citation>Vliet, L. van der, &amp; Ritz, C.
(2013). Statistics for analyzing ecotoxicity test data. In J.-F. Férard
&amp; C. Blaise (Eds.), Encyclopedia of Aquatic Ecotoxicology (pp.
1081–1095). Springer Dordrecht.
https://doi.org/10.1007/978-94-007-5704-2</unstructured_citation>
</citation>
<citation key="Vengateswari2022">
<article_title>Effect of host plants nutrients,
antioxidants, and phytochemicals on growth, development, and fecundity
of spodoptera litura (fabricius) (lepidoptera:
noctuidae)</article_title>
<author>Vengateswari</author>
<journal_title>International Journal of Tropical Insect
Science</journal_title>
<volume>42</volume>
<doi>10.1007/s42690-022-00868-6</doi>
<issn>1742-7592</issn>
<isbn>0123456789</isbn>
<cYear>2022</cYear>
<unstructured_citation>Vengateswari, G., Arunthirumeni, M.,
Shivaswamy, M. S., &amp; Shivakumar, M. S. (2022). Effect of host plants
nutrients, antioxidants, and phytochemicals on growth, development, and
fecundity of spodoptera litura (fabricius) (lepidoptera: noctuidae).
International Journal of Tropical Insect Science, 42, 3161–3173.
https://doi.org/10.1007/s42690-022-00868-6</unstructured_citation>
</citation>
</citation_list>
</journal_article>
</journal>
</body>
</doi_batch>
Binary file added joss.07264/10.21105.joss.07264.pdf
View file
Binary file not shown.
Loading

0 comments on commit d69c141

Please sign in to comment.