source: trunk/doc/historical/specifications/core/annotations.html @ 4509

Last change on this file since 4509 was 4509, checked in by Jari Häkkinen, 15 years ago

Addresses #1106. Missed to change reference wherefrom retrive GPLv3 license text. And some other changes.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Id Date
File size: 4.1 KB
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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: annotations.html 4509 2008-09-11 20:01:44Z jari $
4
5  Copyright (C) 2005 Jari Hakkinen, Nicklas Nordborg
6  Copyright (C) 2006 Jari Hakkinen
7
8  This file is part of BASE - BioArray Software Environment.
9  Available at http://base.thep.lu.se/
10
11  BASE is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License
13  as published by the Free Software Foundation; either version 3
14  of the License, or (at your option) any later version.
15
16  BASE is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19  GNU General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with BASE. If not, see <http://www.gnu.org/licenses/>.
23-->
24<html>
25  <head>
26    <title>BASE - Core specification - Annotations</title>
27  <link rel=stylesheet type="text/css" href="../../styles.css">
28  </head>
29<body>
30
31<div class="navigation">
32  <a href="../../index.html">BASE</a>
33  <img src="../../next.gif">
34  <a href="index.html">Core specification</a>
35  <img src="../../next.gif">
36  Annotations
37</div>
38
39  <h1>Annotations</h1>
40
41  <div class="abstract">
42    <p>
43    This document covers the details of the general annotation
44    system, which BASE uses for annotations of just about anything.
45    </p>
46
47    <b>Contents</b><br>
48    <ol>
49    <li><a href="#annotations">Annotations</a>
50    <li><a href="#types">Annotation types</a>
51    <li><a href="#ontologies">Standard ontologies</a>
52    </ol>
53   
54    <b>See also</b><br>
55    <ul>
56    <li><a href="../../development/overview/data/annotations.html">Implementation overview</a>
57    </ul>
58
59    <p class="authors">
60    <b>Last updated:</b> $Date: 2008-09-11 20:01:44 +0000 (Thu, 11 Sep 2008) $
61    </p>
62  </div>
63
64  <a name="annotations">
65  <h2>1. Annotations</h2>
66  </a>
67
68  <ol>
69  <li>An annotation can be seen as a key-value pair that can be
70    attached to an item.
71
72  <li>A single annotation may have multiple values, how many is
73    controlled by the annotation type (see below).
74
75  <li>Many, but not all, items may be annotated.
76
77  <li>An item may have primary and secondary annotations.
78    A primary annotation is an annotation that was attached
79    directly to that item. A secondary annotation is an annotation
80    that was attached to another item, which is somehow related
81    to the current item.
82
83  <li>Secondary annotations may be picked, one by one, from
84    related items, or as a set of all annotations. If the
85    whole set is picked, new annotations will propagate
86    to the related items.
87
88  <li class="note">[CLIENT] Picking annotations from related items
89    may also be done by copying the related values, and attach them as
90    primary annotations to the current item.
91
92  </ol>
93
94  <a name="types">
95  <h2>2. Annotation types</h2>
96  </a>
97
98  <ol>
99  <li>Each annotation must have a type.
100
101  <li>Annotation types contain information about possible values;
102    either primitive types (int, float, string, etc.) with
103    optional limits, or complex types like ontonlogy terms.
104
105  <li>An annotation type applies to one or more item types (e.g. sample
106    or hybridization).
107
108  <li>Each item may only have one annotation of each annotation type,
109    but, as mentioned above, an annotation may have more than one
110    value.
111
112  <li>Users can define annotation types.
113
114  <li class="question">[QUESTION] Can annotation types be made
115    mandatory, and if so for what subset of items? Per project, maybe?
116
117  <li>It should be possible to flag annotations as
118    required for MIAME compliance.
119
120  </ol>
121
122  <a name="ontologies">
123  <h2>3. Standard ontologies</h2>
124  </a>
125
126  <ol>
127  <li>BASE should be able to import values from standard ontologies
128    like GO and MAGE.
129
130  <li>Those values are used to create annotation types.
131
132  <li>While annotating items, the actual value is be copied, but a reference
133    to the original value should also be maintained. This will
134    make searching less complicated, but also make it possible
135    for a client application to generate warnings or make automatic
136    modifications after an update.
137
138  <li>The core will never automatically update the annotation values
139    if the ontologies are updated.
140
141  </ol>
142
143
144</body>
145</html>
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