forked from oeg-upm/SMART-Protocols
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsp-indexV2.0.htm
executable file
·236 lines (205 loc) · 13.6 KB
/
sp-indexV2.0.htm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
<!--?xml version="1.0" encoding="UTF-8"?-->
<html xmlns="http://www.w3.org/1999/xhtml"><head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<style type="text/css">
/*
This template uses the W3C css for working drafts, with small modiications.
Original copyright:
Copyright 1997-2003 W3C (MIT, ERCIM, Keio). All Rights Reserved.
The following software licensing rules apply:
http://www.w3.org/Consortium/Legal/copyright-software */
/* $Id: base.css,v 1.26 2012/08/31 21:24:31 ijacobs Exp $ */
body {
padding: 2em 1em 2em 70px;
margin: 0;
font-family: sans-serif;
color: black;
background: white;
background-position: top left;
background-attachment: fixed;
background-repeat: no-repeat;
}
:link { color: #00C; background: transparent }
:visited { color: #609; background: transparent }
a:active { color: #C00; background: transparent }
a:link img, a:visited img { border-style: none } /* no border on img links */
a img { color: white; } /* trick to hide the border in Netscape 4 */
@media all { /* hide the next rule from Netscape 4 */
a img { color: inherit; } /* undo the color change above */
}
th, td { /* ns 4 */
font-family: sans-serif;
}
h1, h2, h3, h4, h5, h6 { text-align: left }
/* background should be transparent, but WebTV has a bug */
h1, h2, h3 { color: #005A9C; background: white }
h1 { font: 170% sans-serif }
h2 { font: 140% sans-serif }
h3 { font: 120% sans-serif }
h3 {
border-bottom: 1px solid navy;
margin-top: 3px;
padding-bottom: 5px;
}
h4 { font: bold 100% sans-serif }
h5 { font: italic 100% sans-serif }
h6 { font: small-caps 100% sans-serif }
.hide { display: none }
div.head { margin-bottom: 1em }
div.head h1 { margin-top: 2em; clear: both }
div.head table { margin-left: 2em; margin-top: 2em }
p.copyright { font-size: small }
p.copyright small { font-size: small }
@media screen { /* hide from IE3 */
a[href]:hover { background: #ffa }
}
pre { margin-left: 2em }
p {
margin-top: 0.6em;
margin-bottom: 0.6em;
text-align: justify;
}
dt, dd { margin-top: 0; margin-bottom: 0 } /* opera 3.50 */
dt { font-weight: bold }
ul.toc, ol.toc {
list-style: disc; /* Mac NS has problem with 'none' */
list-style: none;
}
@media aural {
h1, h2, h3 { stress: 20; richness: 90 }
.hide { speak: none }
p.copyright { volume: x-soft; speech-rate: x-fast }
dt { pause-before: 20% }
pre { speak-punctuation: code }
}
/*Additional css*/
.hlist {
background-color: #F4FFFF;
border: 1px solid navy;
padding: 5px;
}
.hlist li {
display: inline-table;
list-style-type: none;
padding-right: 20px;
}
.backlink {
background-color: #F4FFFF;
border: 1px dotted navy;
color: black;
float: right;
font-size: 10pt;
padding: 2px;
text-align: right;
}
.entity {
border: 1px solid navy;
margin: 5px 0;
padding: 5px;
}
table {
background-color: #F4FFFF;
border: 1px solid navy;
margin: 20px;
}
table {
text-align: center;
vertical-align: middle;
}
table td {
padding: 5px 15px;
text-align: left;
}
table th {
background-color: LightGoldenRodYellow;
}
pre {
background-color: #F9F9F9;
border: 1px dashed #2F6FAB;
color: black;
line-height: 1.1em;
padding: 1em;
}
</style>
</head>
<body><div class="head">
<h1>SMART Protocols</h1>
<h2>Release 1 July 2013</h2>
<dl>
<dt>This version:</dt>
<dd><a href="http://www.opmw.org/model/p-plan10112012"> </a> </dd>
</dl><dl><dt>Latest version:</dt>
<dd><a href="http://purl.org/net/SMARTprotocol">http://purl.org/net/SMARTprotocol</a></dd>
</dl><dl>
<dt>Revision</dt>
<dd>Revision 2.0</dd>
</dl><dl><dt>Author:</dt>
<dd><a href="http://oxgiraldo.wordpress.com">Olga Giraldo</a>, Ontology Engineering Group, Universidad Politécnica de Madrid</dd>
</dl><dl><dt>Contributors:</dt>
<dd><a href="http://delicias.dia.fi.upm.es/members/DGarijo/">Daniel Garijo</a>, Ontology Engineering Group, Universidad Politécnica de Madrid</dd>
<dd><a href="http://www.dia.fi.upm.es/index.php?page=oscar-corcho/">Oscar Corcho</a>, Ontology Engineering Group, Universidad Politécnica de Madrid</dd>
<dd><a href="http://www.alexandergarcia.name/">Alexander Garcia</a>, Linkingdata I/O LLC, Fort Collins, Colorado</dd>
</dl><dl>
</dl>
</div>
<div id="toc">
<h2>Table of Contents</h2><ul><li>
<a href="#ontMotivation">1. SMART Protocol Motivation</a></li><li>
<a href="#ontDescription">2. SMART Protocol Description</a></li><li>
<a href="#ontDocumentation">3. Ontology Documentation</a></li><li>
<a href="#references">4. References</a></li><li>
<a href="#acknowledgements">5. Acknowledgements</a></li>
</ul>
</div>
<div id="ontMotivation">
<h2>1. SMART Protocol Motivation <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
<p>In life sciences, experimental protocols provide step-by-step descriptions of procedures. These procedures are the means to verify that the results published in scientific articles are reproducible, instead of being produced at random. A laboratory protocol can be visualized from two perspectives: the protocol as a document and as a workflow. The experimental protocol as a document is published, either inside scientific papers in the materials and methods section or as an independent document. Besides, the protocol is a sequence of tasks and executable operations that includes an input and an output, in this sense a protocol is a type of workflow. However, these experimental protocols may present problems (insufficient granularity in the instructions, ambiguity and/or imprecision) due to the use of natural language. In order to address these problems, we are investigating ways for supporting a more systematic and structured description of protocols to improve the reproducibility of experiments.</p>
</li>
</ul>
</div>
<div id="ontDescription">
<h2>2. SMART Protocol Description <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
<p>The SeMAntic RepresenTation for Protocols, SMART Protocols, provides a structured OWL DL vocabulary of experimental protocols. (<a href="#fig1">Figure 1</a>) shows an overview of the two ontologies that model SMART Protocols. The ontology that describes the experimental protocol as a document is depicted at the top. The class <a style="font-family:'Courier New'">iao:InformationContentEntity</a> and its subclasses (<a style="font-family:'Courier New'">iao:Document, iao:DocumentPart, iao:TextualEntity</a> and <a style="font-family:'Courier New'">iao:DataSet</a>) were imported from The Information Artifact Ontology (<a href="https://code.google.com/p/information-artifact-ontology/">IAO</a>) to represent the document aspects in the protocol. The ontology that describes the experimental protocol as a workflow is depicted at the bottom. The representation of executable aspects of a protocol is captured with the concepts <a style="font-family:'Courier New'">p-plan:Plan, p-plan:Step</a> and <a style="font-family:'Courier New'">p-plan:Variable</a> from P-Plan Ontology (<a href="http://www.opmw.org/model/p-plan10112012/">P-Plan</a>).</p>
<div align="center" id="fig1">
<img src="Imagenes/figure1.png"></src>
<div> <a href="#fig1">Figure 1: </a> SMART Protocols as an extension of the ontologies IAO and P-Plan. The document aspects in a protocol are captured with IAO. The workflow aspects in a protocol are captured with P-Plan. The terms proposed in SMART Protocols use the sp prefix.
</li>
</ul>
</div>
<div id="ontDocumentation">
<h2>3. Ontology Documentation <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
<ul>
<p style="text-align: center;"> <b>The encoding of the SMART Protocols-Document Ontology can be found <a href="docProtocolV2.0.owl"> here </a>. The documentation is available <a href="sp-documentV2.0.htm">here</a></b></p>
<p style="text-align: center;"> <b>The encoding of the SMART Protocols-Workflow Ontology can be found <a href="wfProtocolV2.0.owl"> here </a>The documentation is available <a href="sp-workflowV2.0.htm">here</a></b></p>
<p style="text-align: center;"> <b>The latest encoding of the merged SMART Protocols modules can be found <a href="docWorkflow2.0.owl"> here </a></b></p>
</li>
</ul>
</div>
</div>
<div id="references">
<h2>4. References <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
<ul>
<li id="BFO"><b>[BFO]</b>:Robert Arp and Barry Smith. (2008) <a href="http://precedings.nature.com/documents/1941/version/1/files/npre20081941-1.pdf">
<cite>Function, Role, and Disposition in Basic Formal Ontology</cite></a>. Available from Nature Precedings.</a></li>
<li id="ChEBI"><b>[ChEBI]</b>:Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, and Michael Ashburner. (2008) <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238832/"><cite>ChEBI: a database and ontology for chemical entities of biological interest</cite></a>. Nucleic Acids Res.Vol. 36(Database issue), pages D344–D350.</a></li>
<li id="EXACT"><b>[EXACT]</b>: Larisa N. Soldatova, Wayne Aubrey, Ross D. King and Amanda Clare. (2008).
<cite>The EXACT description of biomedical protocols</cite>.</a> Bioinformatics.Vol. 24 ISMB 2008, pages i295–i303.</a></li>
<li id="IAO"><b>[IAO]</b> <a href="https://code.google.com/p/information-artifact-ontology/"><cite>information-artifact-ontology</cite></a>.</a></li>
<li id="MGEDO"><b>[MGEDO]</b>:Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr. (2006) <a href="http://www.ncbi.nlm.nih.gov/pubmed/16428806"><cite>The MGED Ontology: a resource for semantics-based description of microarray experiments</cite></a>. Bioinformatics. Vol. 1; 22(7), pages 866-73.</a></li>
<li id="MeSH"><b>[MeSH]</b> <a href="http://www.nlm.nih.gov/mesh/meshhome.html"><cite>Medical Subject Headings</cite></a>.</a></li>
<li id="NCI Thesaurus"><b>[NCI Thesaurus]</b> <a href="http://ncit.nci.nih.gov/"><cite>NCI Thesaurus</cite></a>.</a></li>
<li id="NPO"><b>[NPO]</b> <a href="http://www.nano-ontology.org/"><cite>NPO:NanoParticle Ontology for Cancer Nanotechnology Research</cite></a>.</a></li>
<li id="OBI"><b>[OBI]</b>:Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman and Alan Ruttenberg. (2008) <a href="http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/papers/owled2008/owled2008eu_submission_38.pdf"><cite>The OWL of Biomedical Investigations</cite></a>. OWLED.</a></li>
<li id="OBO_REL"><b>[OBO_REL]</b>:Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector and Cornelius Rosse. (2005) <a href="http://genomebiology.com/2005/6/5/R46"><cite>Relations in biomedical ontologies</cite></a>. Genome Biology, Vol. 6:R46.</a></li>
<li id="P-Plan"><b>[P-Plan]</b> <a href="http://www.opmw.org/model/p-plan10112012/"><cite>P-Plan Ontology</cite></a>.</a></li>
<li id="SO"><b>[SO]</b>:Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin and Michael Ashburner. (2005) <a href="http://genomebiology.com/2005/6/5/R44"><cite>The Sequence Ontology: a tool for the unification of genome annotations</cite></a>. Genome Biology, Vol. 6:R44.</a></li>
</ul>
</div>
<div id="acknowledgements">
<h2>5. Acknowledgements <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
<p>
I would like thank <a href="http://www.oeg-upm.net/"> Ontology Engineering Group</a>, <a href="http://www.wf4ever-project.org/"> Wf4Ever</a> project for supporting this research and Silvio Peroni for developing LODE, tool
used to create part of the cross-reference sections of this document.
</p>
</div>
</body></html>