diff --git a/src/test/resources/eml-data-paper.xml b/src/test/resources/eml-data-paper.xml index b104fbf6..83d682a9 100644 --- a/src/test/resources/eml-data-paper.xml +++ b/src/test/resources/eml-data-paper.xml @@ -108,7 +108,7 @@ https://orcid.org/0000-0000-0000-0000 coPrincipalInvestigator - 2018-03-19 + 2018 This project is integrating scientific research in the Arctic with education and outreach, with a strong central focus on engaging undergraduate students and visiting faculty from groups that have had little involvement in Arctic science to date. The central element of the project is a month-long research expedition to the Yukon River Delta in Alaska. The expedition provides a deep intellectual and cultural immersion in the context of an authentic research experience that is paramount for "hooking" students and keeping them moving along the pipeline to careers as Arctic scientists. The overarching scientific issue that drives the research is the vulnerability and fate of ancient carbon stored in Arctic permafrost (permanently frozen ground). Widespread permafrost thaw is expected to occur this century, but large uncertainties remain in estimating the timing, magnitude, and form of carbon that will be released when thawed. Project participants are working in collaborative research groups to make fundamental scientific discoveries related to the vulnerability of permafrost carbon in the Yukon River Delta and the potential implications of permafrost thaw in this region for the global climate system. This data set includes permafrost cores, with ammonium, nitrate, volumetric ice content, N mineralization rates, %C, and %N results from the 2017 expedition. @@ -168,7 +168,13 @@ It can include multiple paragraphs. And these paragraphs should have enough text to wrap in a wide browser. So, repeat that last thought. And these paragraphs should have enough text to wrap in a wide browser. So, repeat that last thought. - And bulleted lists: + Text can also cite other works, such as [@jones_2001], in which case the associated key must be present + as either the citation identifier in a `bibtex` element in the EML document, or as the `id` attribute on + one of the `citation` elements in the EML document. These identifiers must be unique across the document. Tools + such as Pandoc will readily convert these citations and citation entries into various formats, including HTML, PDF, + and others. + + And bulleted lists are also supported: - Science - Engineering @@ -721,20 +727,111 @@ + + + @article{ludwig_2018, + title = {Permafrost carbon and nitrogen, Yukon-Kuskokwim Delta, Alaska}, + url = {http://ecosphere.esa.org/article/yyyy.zzzzzzz}, + doi = {10.xxxx/yyyy.zzzzzz}, + journal = {EcoSphere}, + author = {Ludwig, Sarah}, + year = {2018} + } + + - Title for a paper that used this dataset. - - - Mark - Jarkady - - - 2017 -
- EcoSphere - https://doi.org/10.1002/ecs2.2166 -
+ + @article{jones_2001, + title = {Managing scientific metadata}, + volume = {5}, + issn = {10897801}, + url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=957896}, + doi = {10.1109/4236.957896}, + number = {5}, + journal = {IEEE Internet Computing}, + author = {Jones, Matthew B. and Berkley, Chad and Bojilova, Jivka and Schildhauer, Mark}, + year = {2001}, + pages = {59--68} + } + + + + + @article{fegraus_2005, + title = {Maximizing the {Value} of {Ecological} {Data} with {Structured} {Metadata}: {An} {Introduction} to {Ecological} {Metadata} {Language} ({EML}) and {Principles} for {Metadata} {Creation}}, + journal = {Bulletin of the Ecological Society of America}, + author = {Fegraus, Eric H. and Andelman, Sandy and Jones, Matthew B. and Schildhauer, Mark}, + year = {2005}, + pages = {158--168} + } + + + + Title for a paper that used this dataset. + + + Mark + Jarkady + + + 2017 +
+ EcoSphere + https://doi.org/10.1002/ecs2.2166 +
+ + + @article{hampton_2017, + title = {Skills and {Knowledge} for {Data}-{Intensive} {Environmental} {Research}}, + volume = {67}, + copyright = {All rights reserved}, + issn = {0006-3568, 1525-3244}, + url = {https://academic.oup.com/bioscience/article-lookup/doi/10.1093/biosci/bix025}, + doi = {10.1093/biosci/bix025}, + language = {en}, + number = {6}, + urldate = {2018-02-15}, + journal = {BioScience}, + author = {Hampton, Stephanie E. and Jones, Matthew B. and Wasser, Leah A. and Schildhauer, Mark P. and Supp, Sarah R. and Brun, Julien and Hernandez, Rebecca R. and Boettiger, Carl and Collins, Scott L. and Gross, Louis J. and Fernández, Denny S. and Budden, Amber and White, Ethan P. and Teal, Tracy K. and Labou, Stephanie G. and Aukema, Juliann E.}, + month = jun, + year = {2017}, + pages = {546--557} + } + + @article{brinckman_2018, + title = {Computing environments for reproducibility: {Capturing} the “{Whole} {Tale}”}, + copyright = {All rights reserved}, + issn = {0167739X}, + shorttitle = {Computing environments for reproducibility}, + url = {http://linkinghub.elsevier.com/retrieve/pii/S0167739X17310695}, + doi = {10.1016/j.future.2017.12.029}, + language = {en}, + urldate = {2018-04-16}, + journal = {Future Generation Computer Systems}, + author = {Brinckman, Adam and Chard, Kyle and Gaffney, Niall and Hategan, Mihael and Jones, Matthew B. and Kowalik, Kacper and Kulasekaran, Sivakumar and Ludäscher, Bertram and Mecum, Bryce D. and Nabrzyski, Jarek and Stodden, Victoria and Taylor, Ian J. and Turk, Matthew J. and Turner, Kandace}, + month = feb, + year = {2018} + } + + @article{collins_2018, + title = {Temporal heterogeneity increases with spatial heterogeneity in ecological communities}, + volume = {99}, + copyright = {All rights reserved}, + issn = {00129658}, + url = {http://doi.wiley.com/10.1002/ecy.2154}, + doi = {10.1002/ecy.2154}, + language = {en}, + number = {4}, + urldate = {2018-04-16}, + journal = {Ecology}, + author = {Collins, Scott L. and Avolio, Meghan L. and Gries, Corinna and Hallett, Lauren M. and Koerner, Sally E. and La Pierre, Kimberly J. and Rypel, Andrew L. and Sokol, Eric R. and Fey, Samuel B. and Flynn, Dan F. B. and Jones, Sydney K. and Ladwig, Laura M. and Ripplinger, Julie and Jones, Matt B.}, + month = apr, + year = {2018}, + pages = {858--865} + } + + diff --git a/xsd/eml-dataset.xsd b/xsd/eml-dataset.xsd index 0bf161cd..a81b6327 100644 --- a/xsd/eml-dataset.xsd +++ b/xsd/eml-dataset.xsd @@ -368,6 +368,16 @@ + + + + Reference Publication + A citation to an additional publication that serves as an important reference for a dataset. + A citation to an additional publication that serves as an important reference for a dataset. People using this dataset should generally cite the dataset itself (using the creator, pubDate, title, publisher, and packageId fields), and consider providing an additional citation to the Reference Publication. Common cases where a Reference Publication may be useful include when a data paper is published that describes the dataset, or when a paper is intended to be the canonical or examplar reference to the dataset. + + + + @@ -385,6 +395,20 @@ + + + + Literature Cited + A citation to articles or products which were referenced + in the dataset or its associated metadata. + A citation to articles or products which were referenced + in the dataset or its associated metadata. The list represents the bibliography + of works related to the dataset, whether for reference, comparison, or others + purposes. + + + + diff --git a/xsd/eml-literature.xsd b/xsd/eml-literature.xsd index 241640c2..1d7c048f 100644 --- a/xsd/eml-literature.xsd +++ b/xsd/eml-literature.xsd @@ -103,7 +103,7 @@ Contact An optional contact individual for this citation - The contact field contains information about an alternate person to be contacted + The contact field contains information about an alternate person to be contacted about this citation. Usually, the first author serves as the contact for a citation resource, e.g., a reprint request. In some cases, an alternate individual(s) may serve that function, and can be indicated here. Since contact is of the type rp:ResponsibleParty, a reference may be used. @@ -273,6 +273,16 @@ + + + + Bibtex Citation + Citation in Bibtex format. + The bibtex field provides a parseable citation formatted according to + the Bibtex formatting conventions. The citation entry is assigned a unique key that must be unique across all bibtex fields in the EML document. The citation key can be used in markdown sections of the text to refer to this citation using the pandoc-style of inline citation keys. See the markdown element for more details. The record is delimited using curly braces. Most reference software can both import and export citations in Bibtex format, so this is a simpler representation to produce and consume than native EML citation representations. + + + @@ -1220,4 +1230,28 @@ + + + + + + citation + A citation within a list of citations. + A citation within a list of citations, usually used for a literatureCited + cited list or similar. Each citation is formatted following the EML CitationType + structure. + + + + + + + Bibtex Citation List + List of citations in Bibtex format. + The bibtex field provides a parseable list of citations formatted according to the Bibtex formatting conventions. Each citation entry is assigned a unique key that must be unique across all bibtex fields in the EML document. The citation key can be used in markdown sections of the text to refer to this citation using the pandoc-style of inline citation keys. See the markdown element for more details. The record is delimited using curly braces. Most reference software can both import and export citations in Bibtex format, so this is a simpler representation to produce and consume than native EML citation representations. + + + + + diff --git a/xsd/eml-text.xsd b/xsd/eml-text.xsd index 39b894a3..3c09e6d0 100644 --- a/xsd/eml-text.xsd +++ b/xsd/eml-text.xsd @@ -132,7 +132,7 @@ markdown reference syntax, for example ![Figure 1][fig.1.ab567w], where "fig.1.ab567w" is the unique id attribute for the entity containing the reference to the image. When client tools process such image links, they should inline the image data from that entity at the - location specified, which may involve , for example, resolving the image url from an + location specified, which may involve, for example, resolving the image url from an otherEntity section. This means that there is an implied link in all Markdown documents of the form [id]: url/to/image "Optional title attribute", which is derived from the metadata for each entity within a document. Users do not need to insert these links in @@ -140,6 +140,27 @@ need to generate them from the entity metadata if they are using an external Markdown pre-processor to handle conversion to HTML and other languages. + + Inline citations can also be used to cite scholarly works in the text of an EML + document. This follows the Pandoc syntax for citation keys, in which the citation keys + are in inside square brackets and separated by semicolons. Each citation is identified + by a key, which consists of an ‘@’ symbol and the citation identifier from the entry for + that citation. Citation keys may optionally have a prefix, a locator, and a suffix to + further qualify what is being cited. For example, a simple citation would be + constructed as '[@fegraus_2005]', and a list would be '[@jones_2001; @fegraus_2005]'. + The keys must be present in either the 'id' field of a + citation element in the EML document, or as the BibTex key in a 'bibtex' entry in the + EML document. It is a validation error to cite an entry for which the corresponding + citation key is not present in the EML document, and it is a validation error for the + same citation key to be reused across citation and bibtex elements in the document (each + citation identifier must be unique within the document). Clients that parse and display + EML documents should first gather up all citation and bibtex elements in the document to + create a citation database in bibtext format, and then pass that database along with the + text in markdown sections to pandoc or an equivalent tool to convert the citations into + properly formatted, human readable citations. Pandoc supports the use of Citation Style + Language (CSL) files to specify the formatting of citations upon conversion. See + http://citationstyles.org/ for more details. + Because bulleted lists and other structures within Markdown are dependent on indenting the raw markdown text, authors and processors should pay close attention to formatting within the