source: trunk/doc/historical/specifications/core/reporters.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: 4.2 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: reporters.html 4509 2008-09-11 20:01:44Z jari $
4
5  Copyright (C) 2005 Samuel Andersson, 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 - Reporters</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  Reporters
37</div>
38
39  <h1>Reporters</h1>
40
41  <div class="abstract">
42    <p>
43    This document covers the details of how reporters (clones, oligos,
44      etc.) are handled by BASE.
45    </p>
46
47    <b>Contents</b><br>
48    <ol>
49    <li><a href="#reporters">Reporters</a>
50    </ol>
51
52    <b>See also</b><br>
53    <ul>
54    <li><a href="../../development/overview/data/reporters.html">Implementation overview</a>
55    </ul>
56
57    <p class="authors">
58    <b>Last updated:</b> $Date: 2008-09-11 20:01:44 +0000 (Thu, 11 Sep 2008) $
59    </p>
60  </div>
61
62  <a name="biomaterials">
63  <h2>1. Reporters</h2>
64  </a>
65
66  <ol>
67  <li>A reporter represents (the idea of) a clone, oligo, or other
68    reporter for a gene.
69
70  <li>Every reporter has a unique reporter id, which is a string.
71
72  <li>Every reporter may, but doesn't have to, have a type.
73    The type is mainly used for easier filtering of reporters.
74
75  <li>A reporter has a gene name and a gene symbol (short name).
76
77  <li>The server admin may add additional columns to the table
78    and tell BASE about them; what type they have, what they
79    represent, and so on. These columns should then appear in
80    BASE wherever one would expect them to.
81
82  <li>Information about the additional columns of the reporter
83    table is stored in an XML file.
84
85  <li><span class="invalid">The server admin should also be able to define
86    connections to
87    external tables (possibly in another database, if the RDBMS
88    supports it). For each such table, BASE needs to know how to
89    construct a JOIN (what to join on and whether to use LEFT
90    JOIN), and what the available columns in that table are.
91    </span>
92    <div class="note">[NOTE] If this is desired, please choose a database
93    system which has the functionality of mapping remote tables into local
94    ones, and define views to make it all appear as one table for the
95    BASE core. Of course, insertions and deletions must also be supported
96    by the setup.
97    </div>
98
99  <li class="invalid">It should be possible to use the external tables when filtering
100    reporters, and values from the external tables may be retrieved
101    as part of searches.
102
103  <li class="invalid">Some external databases have a version number, e.g. ACID with
104    different UniGene builds. BASE does not need to have any awareness
105    of this. Instead, different versions should be seen as different
106    external databases. If an external database is removed, BASE
107    should be notified about it, and if a user tries to re-run an
108    old search against this database, a meaningful error should be
109    generated.
110
111  <li class="note">[CLIENT] It should be possible to construct links to
112    external resources
113    (identified by URIs) with reporter information, using the
114    reporter id and possibly other reporter information. As reporters
115    may come from different sources, these rules for constructing
116    links should be data dependent. Regexps may be useful for this.
117
118  <li><span class="invalid">The reporter whose reporter id is an empty string is always
119    supposed to exist, and its reporter id should not be changed.
120    This reporter is used to represent a lack of reporter material,
121    for instance for empty plate wells.</span> Use NULL values for this
122    instead.
123
124  </ol>
125
126</body>
127</html>
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