From 46d63a8a48b552ebde62bb02bde7314336e51f5c Mon Sep 17 00:00:00 2001 From: mh17 <mh17> Date: Wed, 3 Mar 2010 13:56:42 +0000 Subject: [PATCH] reorganisings docs --- doc/ZMAP_LACE_XML.README | 211 --------------------------------------- 1 file changed, 211 deletions(-) delete mode 100755 doc/ZMAP_LACE_XML.README diff --git a/doc/ZMAP_LACE_XML.README b/doc/ZMAP_LACE_XML.README deleted file mode 100755 index b2ceabc0a..000000000 --- a/doc/ZMAP_LACE_XML.README +++ /dev/null @@ -1,211 +0,0 @@ -ZMap - lace XML communication -============================= - - -The following describes changes to zmap and changes that need to be made -to otterlace to support feature display. - - -Overall structure ------------------ - -My original (= naive) approach was that there would be some pages prepared by -zmap and some by lace but actually this won't work if we are to produce what -the annotators would like. - -We need to have pages that are mixtures of zmap and lace stuff. - - -To support this I have introduced "subsection"s so that canonical xml looks -like this (I've omitted the attributes and data for clarity): - - -<zmap> - <response> - <notebook> - <chapter> - - <!-- this the only bit that otter needs to address... --> - <page> - <subsection> - <paragraph> - <tagvalue> - </tagvalue> - </paragraph> - </subsection> - </page> - - </chapter> - </notebook> - </response> -</zmap> - - -The notebook and chapter parts need not be named because for feature display -there will only be one notebook with one chapter. - - - -Merging -------- - -Otterlace will need to send over a mixture of its own complete pages and also -subsections to be displayed on existing pages. zmap will merge both into the -feature display notebook. - -At the moment I am not proposing to support merging at the paragraph level as -this introduces a number of semantic problems that I think we can avoid by -simply saying that merging will only be supported from paragraphs upwards. - -The merging will require that we have an agreed set of names for any pages, -subsections etc that are to be merged. We could have some incredibly dynamic -system where zmap passes the names to lace and then lace passes them back but -I think this is overkill and we should just agree on the names. The examples -below will show currently supported names. - - - -New TagValue types ------------------- - -I have added multicolumn lists which require synchronisation between the -paragraph and its tagvalues, an example will clarify: - -Let's assume we have a 3 column list consisting of start, end and ID data, -here's an example of how to specify this: - -<paragraph name="Exon" type="compound_table" - columns="'start' 'end' 'StableID'" column_types="int int string"> - - <tagvalue type="compound">43491 43674 OTTHUME00000336182</tagvalue> - <tagvalue type="compound">41283 41369 OTTHUME00000336156</tagvalue> - <tagvalue type="compound">37289 37374 OTTHUME00000336151</tagvalue> - - etc - -</paragraph> - -"columns" is mandatory and gives the titles for the columns - -"column_types" is mandatory and gives the datatype for the column - -The number of values in the "compound" tagvalues must match the number of -columns. - - - -Alignment Display ------------------ - -XML data for requests for alignments from zmap should include: - - -<response handled="true"> - - <!-- note that notebook and chapter are anonymous. --> - <notebook> - <chapter> - - - <!-- Predefined page name....only need to include this if below data exists - for this alignment. --> - <page name="Details"> - - <!-- Predefined subsection name. --> - <subsection name="Align"> - - <paragraph type="tagvalue_table"> - <tagvalue name="Accession" type="simple">accession number of match sequence</tagvalue> - </paragraph> - - <paragraph type="tagvalue_table"> - <tagvalue name="Title" type="simple">title from "Visible Title" tags in acedb</tagvalue> - </paragraph> - - </subsection> - - </page> - - </chapter> - </notebook> -</response> - - - - -Transcript Display ------------------- - -XML data for requests for transcripts from zmap should include: - -<response handled="true"> - - <!-- note that notebook and chapter are anonymous. --> - <notebook> - <chapter> - - - <!-- Predefined page name....only need to include this if Locus etc exist - for this feature. --> - <page name="Details"> - - <!-- Predefined subsection name. --> - <subsection name="Feature"> - - <paragraph name="Locus" type="tagvalue_table"> - <tagvalue name="Symbol" type="simple">short/object name</tagvalue> - <tagvalue name="Full Name" type="simple">longer descriptive name</tagvalue> - </paragraph> - - </subsection> - - - <!-- Predefined subsection name, only need to include this if there is a remark - and supporting evidence. --> - <subsection name="Annotation"> - - <paragraph type="simple"> - <tagvalue name="Remark" type="scrolled_text">some kind of description</tagvalue> - </paragraph> - - <paragraph name="Evidence" type="tagvalue_table"> - <tagvalue name="Trembl" type="simple">XXXXX.4</tagvalue> - <tagvalue name="EST" type="simple">sdkfjsdlkfjsljk.41</tagvalue> - </paragraph> - - </subsection> - - </page> - - - - <!-- this page is completely Otters so you can change the title, names etc - as you like --> - <page name="Otter"> - <subsection name="Stable IDs"> - <paragraph name="Gene" type="tagvalue_table"> - <tagvalue name="Stable ID" type="simple">OTTHUMG00000031177</tagvalue> - </paragraph> - <paragraph name="Transcript" type="tagvalue_table"> - <tagvalue name="Stable ID" type="simple">OTTHUMT00000076345</tagvalue> - </paragraph> - <paragraph name="Exon" type="compound_table" columns="'start' 'end' 'StableID'" - column_types="int int string"> - <tagvalue type="compound">43491 43674 OTTHUME00000336182</tagvalue> - <tagvalue type="compound">41283 41369 OTTHUME00000336156</tagvalue> - - etc.... - - <tagvalue type="compound">29356 29460 OTTHUME00001470549</tagvalue> - </paragraph> - </subsection> - </page> - - - </chapter> - </notebook> -</response> - - - - -- GitLab