{"action":"created","issue":{"url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed/issues/61","repository_url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed","labels_url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed/issues/61/labels{/name}","comments_url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed/issues/61/comments","events_url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed/issues/61/events","html_url":"https://github.com/elifesciences/elife-pubmed-feed/issues/61","id":264868604,"node_id":"MDU6SXNzdWUyNjQ4Njg2MDQ=","number":61,"title":"Adding dataset 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future, it would be good to take anything listed in the Major datasets generated section:\r\n\r\n ```\r\nxml\r\n<sec sec-type=\"datasets\" id=\"s7\">\r\n                <title>Major datasets</title>\r\n                <p>The following datasets were generated:</p>\r\n                <p>\r\n                    <related-object content-type=\"generated-dataset\"\r\n                        source-id=\"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73147\"\r\n                        source-id-type=\"uri\" id=\"dataset1\">\r\n                        <collab collab-type=\"author\">Mishra A</collab>\r\n                        <collab collab-type=\"author\">Pisco AO</collab>\r\n                        <collab collab-type=\"author\">Watt FM</collab>\r\n                        <year>2017</year>\r\n                        <source>A protein phosphatase network controls the temporal and spatial\r\n                            dynamics of differentiation commitment in human epidermis</source>\r\n                        <ext-link ext-link-type=\"uri\"\r\n                            xlink:href=\"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73147\"\r\n                            >https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73147</ext-link>\r\n                        <comment>Publicly available at the NCBI Gene Expression Omnibus (accession\r\n                            no. GSE73147)</comment>\r\n                    </related-object>\r\n                </p>\r\n                <p>\r\n                    <related-object content-type=\"generated-dataset\"\r\n                        source-id=\"http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD003281\"\r\n                        source-id-type=\"uri\" id=\"dataset2\">\r\n                        <collab collab-type=\"author\">Mishra A</collab>\r\n                        <collab collab-type=\"author\">Pisco AO</collab>\r\n                        <collab collab-type=\"author\">Watt FM</collab>\r\n                        <year>2017</year>\r\n                        <source>A protein phosphatase network controls the temporal and spatial\r\n                            dynamics of differentiation commitment in human epidermis</source>\r\n                        <ext-link ext-link-type=\"uri\"\r\n                            xlink:href=\"http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD003281\"\r\n                            >http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD003281</ext-link>\r\n                        <comment>Publicly available at ProteomeXchange (accession no.\r\n                            PXD003281)</comment>\r\n                    </related-object>\r\n                </p>\r\n            </sec>\r\n```\r\n\r\nand convert, example:\r\n```\r\nxml\r\nFor example:\r\n<Object Type=\"NCBI:geo\">\r\n<Param Name=\"id\">GSE73147</Param>\r\n</Object>\r\n```\r\n\r\nHowever, in this section I don't think we are storing the information in a way it can be parsed for this data, WDYT @gnott ? This links t the work ongoing regarding Data Availability Statements.\r\n\r\nPlan I have as at Feb 1, 2019:\r\n\r\n- [x] Parse the `assigning-authority` value from datasets in the article XML as a new value in the datasets JSON output named `assigningAuthority`\r\n- [x] Also may want to enhance the parser to extract `dataId` values from the `pub-id` tag when appropriate (currently it only takes them from `object-id` `\"art-access-id\"` type tags)\r\n- [x] Add a new property to the `elife-article` `Dataset` object, something like `assigning_authority`\r\n- [x] Parse from the datasets JSON the `assigningAuthority` value to populate `Dataset` objects `assigning_authority` value when parsing from XML to eLife article objects\r\n- [ ] In `elife-pubmed-xml-generation`, add `<Object>` tags for the datasets, including either the DOI value or accession id / dataId value, as is specified in the original article XML"},"comment":{"url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed/issues/comments/463007941","html_url":"https://github.com/elifesciences/elife-pubmed-feed/issues/61#issuecomment-463007941","issue_url":"https://api.github.com/repos/elifesciences/elife-pubmed-feed/issues/61","id":463007941,"node_id":"MDEyOklzc3VlQ29tbWVudDQ2MzAwNzk0MQ==","user":{"login":"gnott","id":1779115,"node_id":"MDQ6VXNlcjE3NzkxMTU=","avatar_url":"https://avatars1.githubusercontent.com/u/1779115?v=4","gravatar_id":"","url":"https://api.github.com/users/gnott","html_url":"https://github.com/gnott","followers_url":"https://api.github.com/users/gnott/followers","following_url":"https://api.github.com/users/gnott/following{/other_user}","gists_url":"https://api.github.com/users/gnott/gists{/gist_id}","starred_url":"https://api.github.com/users/gnott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gnott/subscriptions","organizations_url":"https://api.github.com/users/gnott/orgs","repos_url":"https://api.github.com/users/gnott/repos","events_url":"https://api.github.com/users/gnott/events{/privacy}","received_events_url":"https://api.github.com/users/gnott/received_events","type":"User","site_admin":false},"created_at":"2019-02-13T00:53:30Z","updated_at":"2019-02-13T00:53:30Z","author_association":"MEMBER","body":"Drafting the logic in the https://github.com/elifesciences/elife-pubmed-xml-generation library, I have some details and questions.\r\n\r\n**Current status**: Using the latest kitchen sink XML, https://github.com/elifesciences/XML-mapping/blob/master/elife-00666.xml, as the example, here is the new XML included in the Pubmed deposit for the datasets:\r\n\r\n```\r\n<Object Type=\"Dryad\">\r\n    <Param Name=\"id\">10.5061/dryad.kj1f3v4</Param>\r\n</Object>\r\n<Object Type=\"NCBI\">\r\n    <Param Name=\"id\">GSE48760</Param>\r\n</Object>\r\n```\r\n\r\nThis includes only `doi` and `accession_id` values of the `Dataset` object. \r\n\r\nI tried including the `uri` value of the third dataset which has the `assigning_authority` of `\"other\"` in the XML, however since `other` is not a value Pubmed will accept, I've omitted including any plain `uri` yet, not having a good example use case. Fortunately, if Pubmed does not recognise the value in the `<Object>` tag's `Type` attribute, it just ignores it and does not cause any errors on their deposit validation tool.\r\n\r\n**Issue/question 1:** Regarding `<Object Type=\"NCBI\">`, it is not on the accepted value list specified by Pubmed. If I change it to `<Object Type=\"NCBI:geo\">` then Pubmed does display it. @Melissa37, will you be providing more specific NCBI assigning authority values in the XML? If not, do you know how we can determine and include the `:geo` portion of the `Type` name?\r\n\r\n**Issue/question 2:** The example with `<Object Type=\"Dryad\">` seems to work correctly, it shows like this:\r\n\r\n![image](https://user-images.githubusercontent.com/1779115/52678430-7ca42a00-2ee6-11e9-8030-9f872321b47a.png)\r\n\r\nDo you have examples of datasets that would be `Figshare` type, and will those also have a DOI value? Are there other examples of dataset `<pub-id>` tags you could share that are possible to add to the Pubmed deposits?\r\n\r\n\r\n"}}
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