{"action":"created","issue":{"url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/issues/6","repository_url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations","labels_url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/issues/6/comments","events_url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/issues/6/events","html_url":"https://github.com/SynBioDex/SBOLv-realizations/issues/6","id":244798931,"number":6,"title":"SEP V003: Distinguished Unknowns","user":{"login":"jakebeal","id":10675899,"avatar_url":"https://avatars3.githubusercontent.com/u/10675899?v=4","gravatar_id":"","url":"https://api.github.com/users/jakebeal","html_url":"https://github.com/jakebeal","followers_url":"https://api.github.com/users/jakebeal/followers","following_url":"https://api.github.com/users/jakebeal/following{/other_user}","gists_url":"https://api.github.com/users/jakebeal/gists{/gist_id}","starred_url":"https://api.github.com/users/jakebeal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jakebeal/subscriptions","organizations_url":"https://api.github.com/users/jakebeal/orgs","repos_url":"https://api.github.com/users/jakebeal/repos","events_url":"https://api.github.com/users/jakebeal/events{/privacy}","received_events_url":"https://api.github.com/users/jakebeal/received_events","type":"User","site_admin":false},"labels":[{"id":655380518,"url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/labels/Draft","name":"Draft","color":"fbca04","default":false},{"id":655379505,"url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/labels/SEP","name":"SEP","color":"0e8a16","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2017-07-21T22:35:19Z","updated_at":"2017-07-26T16:29:34Z","closed_at":null,"body":"# SEP V003: Distinguished Unknowns\r\n\r\n| SEP | <leave empty> |\r\n| --- | --- |\r\n| **Authors** | Jacob Beal (jakebeal@ieee.org) |\r\n| **Editor** | <leave empty> |\r\n| **Type** | Specification |\r\n| **SBOL Visual Version** | 1.1 |\r\n| **Status** | Draft |\r\n| **Created** | 21-Jul-2017 |\r\n| **Last modified** | <leave empty if this is the first submission> |\r\n## Abstract\r\n\r\nWe need a way of distinguishing between three distinct use cases that are currently all covered by the \"User Defined\" symbol.  These are:\r\n\r\n* Unspecified: SO:0000110 Sequence Feature\r\n* No glyph assigned: Any SO term that is not covered by any glyph besides the root Sequence Feature\r\n* Composite: SO:0000804 Engineered Region\r\n\r\nAccompanying with the Composite proposal is also a proposal for an Omitted Detail glyph explicitly showing where information is not being represented.\r\n\r\n## Table of Contents  <remove TOC if SEP is rather short>\r\n- [1. Rationale](#rationale) \r\n- [2. Specification](#specification)\r\n- [3. Example or Use Case](#example)\r\n- [4. Backwards Compatibility](#compatibility)\r\n- [5. Discussion](#discussion)\r\n- [References](#references)\r\n- [Copyright](#copyright)\r\n\r\n## 1. Rationale <a name=\"rationale\"></a>\r\n\r\nImporting large numbers of constructs has found three distinct cases that need to be visually distinguished but currently are all lumped under 'User Defined\":\r\n\r\n* \"Unspecified\": Constructs whose type information is missing --- here called \"Unspecified,\" and typically defaulting to the root term SO:0000110.  Here, we want people to recognize the problem and fill in the missing information.\r\n* \"No Glyph Assigned\": Constructs with a well-defined and interesting type that happens to not be covered by any of the current glyphs. Here, we want people to recognize that the part is well understood, just outside the current vocabulary. We also want them to make new glyph proposals.\r\n* \"Composite\": Potentially complex designs composing multiple parts. Here we want to have people recognize that there is more detail available.\r\n\r\nThe Unspecified glyph is intended for showing where a sequence's role is missing (or, equivalently, given only the uninformative \"Sequence Feature\" root role). It should never appear with well-curated designs or diagrams.\r\n\r\nNo Glyph Assigned is intended for constructs with a defined specific role that happens to not yet be covered by available approved glyphs (other than the root \"Sequence Feature\"). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose.\r\n\r\nSome of the proposed glyphs for Composite are linked to the proposal for an Omitted Detail glyph.\r\n\r\n## 2. Specification <a name=\"specification\"></a>\r\n\r\nThe \"User Defined\" glyph will be split into three new glyphs: \"Unspecified\", \"No Glyph Assigned\", and \"Composite\".\r\n\r\nA number of proposals have been made for these glyphs, from which we need to pick one to be RECOMMENDED for each and may choose to pick others as alternatives.\r\n\r\nCurrently, all three of these meanings are covered by the \"User Defined\" glyph, a plain rectangle suggesting a blank slate to be written upon:\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/user-defined-specification.png)\r\n\r\n### Unspecified and No Glyph Assigned \r\n\r\nA number of potential replacement glyphs and variants have been proposed for covering Unspecified and/or No Glyph Assigned.  These are:\r\n\r\n* The unicode \"replacement character\" glyph, indicating a missing or invalid symbol:\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/replacement-glyph-specification.png)\r\n* A tall thin rectangle, which some fonts use as an alternative \"replacement character\":\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/tall-rectangle-specification.png)\r\n* A piece of DNA: \r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/dna-specification.png)\r\n* A horizontal line:\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/blank-line-specification.png)\r\n* A horizontal line with a question mark over it:\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/blank-line-question-specification.png)\r\n* A dashed line rectangle, implying something is missing:\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/dashed-rectangle-specification.png)\r\n* A rectangle with an X through it:\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/X-rectangle-specification.png)\r\n* A half-rounded rectangle, the SBGN glyph for a nucleic acid:\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/halfround-rectangle-specification.png)\r\n\r\n\r\n### Composite \r\n\r\nFor Composite the following glyphs have been proposed:\r\n\r\n* Dashed \"expanding lines\" connecting an Omitted glyph (one candidate shown here for an example) to a backbone diagramming the contents of the composite. Note this glyph's bounding box is only the Omitted glyph.\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/composite-omitted-detail-specification.png)\r\n\r\n* Dashed \"expanding lines\" connecting a point of the backbone to a backbone diagramming the contents of the composite.  Note that this glyph has no bounding box.\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/composite-point-specification.png)\r\n* Dashed \"expanding lines\" connecting two bars to a backbone diagramming the contents of the composite. Note that this glyph has no bounding box.\r\n\r\n  ![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/composite-bars-specification.png)\r\n* A double rectangle:\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/double-box-specification.png)\r\n\r\n* A \"black box\":\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/user-defined/black-box-specification.png)\r\n\r\n### Omitted Detail\r\n\r\nNo SO term will be associated with this, as it is indicating that something is *not* being representing.\r\n\r\nThe proposed omitted detail glyphs all are a break in the backbone with something to indicate that material would normally be in that location, e.g., an ellipsis:\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/omitted-detail/omitted-detail-ellipsis-specification.png)\r\n\r\nor brackets:\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/omitted-detail/omitted-detail-brackets-specification.png)\r\n\r\nor a straight or slanted \"graph axis break\":\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/omitted-detail/omitted-detail-slanted-specification.png)\r\n\r\n![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOLv-realizations/8423527/Glyphs/omitted-detail/omitted-detail-straight-specification.png)\r\n\r\nAll of these glyphs actually place a \"break\" in the nucleic acid backbone.\r\n\r\n## 3. Examples <a name='example'></a>\r\n\r\nUnspecified: an anonymous sequence that is missing any information about its nature or intended purpose.\r\n\r\nNo Glyph Assigned is intended to be used for any Component that is not covered by other SBOL Visual glyphs.\r\n\r\nComposite: an \"expression cassette\" containing a ribosome entry site, coding sequence, and terminator.\r\n\r\nOmitted Detail: A diagram in which a sequence features is not drawn.\r\n\r\n## 4. Backwards Compatibility <a name='compatibility'></a>\r\n\r\nThe \"User Defined\" rectangle will remain as a RECOMMENDED or alternative glyph for all three glyphs.\r\n\r\n## 5. Discussion <a name='discussion'></a>\r\n\r\n## Copyright <a name='copyright'></a>\r\n\r\n<p xmlns:dct=\"http://purl.org/dc/terms/\" xmlns:vcard=\"http://www.w3.org/2001/vcard-rdf/3.0#\">\r\n  <a rel=\"license\"\r\n     href=\"http://creativecommons.org/publicdomain/zero/1.0/\">\r\n    <img src=\"http://i.creativecommons.org/p/zero/1.0/88x31.png\" style=\"border-style: none;\" alt=\"CC0\" />\r\n  </a>\r\n  <br />\r\n  To the extent possible under law,\r\n  <a rel=\"dct:publisher\"\r\n     href=\"sbolstandard.org\">\r\n    <span property=\"dct:title\">SBOL developers</span></a>\r\n  has waived all copyright and related or neighboring rights to\r\n  <span property=\"dct:title\">SEP 002</span>.\r\nThis work is published from:\r\n<span property=\"vcard:Country\" datatype=\"dct:ISO3166\"\r\n      content=\"US\" about=\"sbolstandard.org\">\r\n  United States</span>.\r\n</p>"},"comment":{"url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/issues/comments/318108362","html_url":"https://github.com/SynBioDex/SBOLv-realizations/issues/6#issuecomment-318108362","issue_url":"https://api.github.com/repos/SynBioDex/SBOLv-realizations/issues/6","id":318108362,"user":{"login":"bbartley","id":2539464,"avatar_url":"https://avatars2.githubusercontent.com/u/2539464?v=4","gravatar_id":"","url":"https://api.github.com/users/bbartley","html_url":"https://github.com/bbartley","followers_url":"https://api.github.com/users/bbartley/followers","following_url":"https://api.github.com/users/bbartley/following{/other_user}","gists_url":"https://api.github.com/users/bbartley/gists{/gist_id}","starred_url":"https://api.github.com/users/bbartley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bbartley/subscriptions","organizations_url":"https://api.github.com/users/bbartley/orgs","repos_url":"https://api.github.com/users/bbartley/repos","events_url":"https://api.github.com/users/bbartley/events{/privacy}","received_events_url":"https://api.github.com/users/bbartley/received_events","type":"User","site_admin":false},"created_at":"2017-07-26T16:29:34Z","updated_at":"2017-07-26T16:29:34Z","body":"@jakebeal yes, I like that generalization! "}}
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