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Dear Plant Ontology curators.<br>
<br>
<i>[ This email is being sent at the request of the OBO Foundry
coordinators Barry Smith, Suzi Lewis, Chris Mungall and Michael
Ashburner]</i><br>
<br>
I am approaching you regarding your role as an editor/curator of the
following
ontologies:<br>
<b>Plant growth and developmental stage ,
<a class="moz-txt-link-freetext" href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_temporal">http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_temporal</a><br>
Plant structure<span style=""> ,
<a class="moz-txt-link-freetext" href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_anatomy">http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_anatomy</a></span></b><br>
<a class="moz-txt-link-freetext"
href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncithesaurus"></a><br>
This is an opportunity for you and your ontology community to <b>help
OBO
Foundry</b><b> shape </b><b>guidelines for naming conventions</b>.<br>
I would appreciate <b>your input to our survey</b> on your current
practice
in naming (labeling) entities within your ontology.<br>
The questionnaire is copied below and it is also available at the OBO
Foundry
wiki <a class="moz-txt-link-freetext"
href="http://obofoundry.org/wiki/index.php/Naming">http://obofoundry.org/wiki/index.php/Naming</a>
<br>
<br>
Please, fill out the attached <b>questionnaire </b>and send it back
to me,
or alternatively let me know if you are available for a <b>phone </b>or
<b>skype
interview </b>and your contact details.<br>
<br>
The first phase of the survey has been completed and we have already
collected
answers fr<font color="#000000">om<b> 34 </b>ontol</font>ogies!<br>
This second and last part of the survey will be closed by Feb 8th and
results posted at the OBO Foundry wiki page.<br>
<br>
If you have any question, please don’t hesitate to contact me. Thanks
in
advance for your reply! <br>
<br>
Best regards, <br>
Daniel Schober <br>
<b><br>
<font color="#000000">***<br>
The OBO Foundry paper is out in Nature Biotechnology<br>
<a class="moz-txt-link-freetext"
href="http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf">http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf</a><br>
****</font></b><br>
<br>
<br>
<br>
<h1 style="text-align: center; line-height: 150%;" align="center"><u><span
style="font-size: 14pt; line-height: 150%; text-transform: uppercase; font-weight: normal;">naming
conventions - SURVEY<o:p></o:p></span></u></h1>
<h3 style="text-align: justify; line-height: 150%;"><span
style="font-size: 14pt; line-height: 150%; font-weight: normal;">Scope<o:p></o:p></span></h3>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-family: Arial;">The overall goals of this survey are
twofold:<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-left: 36pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-family: Arial;"><span style="">1.<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span style="font-family: Arial;">to
evaluate the current practice in naming entities within the OBO
ontology
working groups<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-left: 36pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-family: Arial;"><span style="">2.<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span style="font-family: Arial;">to
move towards a common set of naming convention for the OBO Foundy<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-family: Arial;">Further details on the rationale for this
survey
can be found in Schober <i style="">et al</i>. 2007, “<span style="">Towards
naming conventions for use in controlled vocabulary and ontology
engineering”, </span><u><a
href="http://bio-ontologies.org.uk/download/Bio-Ontologies2007.pdf">http://bio-ontologies.org.uk/download/Bio-Ontologies2007.pdf</a></u>,
pages 29-32.<o:p></o:p></span></p>
<h3 style="text-align: justify; line-height: 150%;"><span
style="font-size: 14pt; line-height: 150%; font-weight: normal;">Results<o:p></o:p></span></h3>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-family: Arial;">Any questions as well as the completed
questionnaires should be sent to Daniel Schober (<a
class="moz-txt-link-abbreviated" href="mailto:schober@ebi.ac.uk">schober@ebi.ac.uk</a>).
The outcome will be posted on the OBO Foundry wiki pages (</span><a
class="moz-txt-link-freetext"
href="http://obofoundry.org/wiki/index.php/Naming">http://obofoundry.org/wiki/index.php/Naming</a>)
<span style="font-family: Arial;">and all participants will get
notified accordingly.<o:p></o:p></span></p>
<span style="font-family: Arial;"><o:p></o:p></span><i style=""><span
style="font-family: Arial;"></span></i><span
style="font-family: Arial;"><o:p></o:p></span>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 14pt; line-height: 150%; font-family: Arial;">Questionnaire</span><span
style="font-family: Arial;"><o:p></o:p></span></p>
<h3 style="text-align: justify; line-height: 150%;"><u>1. Questions on
your ontology and its engineering and maintenance process<o:p></o:p></u></h3>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">1.1 </span></b><span
style="font-family: Arial;">Are you and your co-workers familiar with
the
OBO Foundry principles (<a href="http://www.obofoundry.org/crit.shtml">http://www.obofoundry.org/crit.shtml</a>)?
<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"> </p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">1.2</span></b><span
style="font-family: Arial;"> If yours in an OBO Foundry ontology, have
you started implementing these principles and aligned your development
process accordingly?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-family: Arial;"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">1.3</span></b><span
style="font-family: Arial;"> Is work on your ontology closely
associated
with the need to manage and formulate queries about a specific body of
data?
If so, can you specify the type of data? <o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">This
question
refers to the instance level and annotated data bodies. Is the ontology
developed
in collaboration with the maintenance of a database or collection of
databases
(as the GO is developed in collaboration with UniProt and with various
MOD
databases)?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">1.4</span></b><span
style="font-family: Arial;"> Which ontology editor tool(s) do you use
to
build and manage your ontology?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">1.5 </span></b><span
style="font-family: Arial;">Please illustrate the editing process,
i.e.
is your ontology developed in a centralised or distributed manner? In
both
cases, please, state the number of people directly handling and editing
the
ontology file and if they are physically distributed or if they are
located
in one spot. <o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">1.6</span></b><span
style="font-family: Arial;"> Do you introduce special <i style="">helper
classes</i> or <i style="">bins</i>, that refer to metadata to
facilitate
the engineering process? If yes, please describe them and explain how
do
you indicate their special status?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">Examples
are ‘obsolete classes’, ‘imported classes’, ‘deleted classes’.<o:p></o:p></span></p>
<h3 style="text-align: justify; line-height: 150%;"><u>2. General
questions
on your current practice in naming entities and their documentation<o:p></o:p></u></h3>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">2.1</span></b><span
style="font-family: Arial;"> Have you developed naming conventions
within
your ontology community? If yes, please specify how these are
formulated, e.g. as a specific, standalone document or as part of other
documentation
and where these are available, e.g. provide URL. <o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">2.2 </span></b><span
style="font-family: Arial;">(If your answer to 2.1 is positive)</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"> </span><span
style="font-family: Arial;">Which entities are tackled by your naming
conventions?</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">Some
examples
are provided below, add if required</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">:<o:p></o:p></span></p>
<ul style="margin-top: 0cm;" type="disc">
<li class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">class
names <o:p></o:p></span></li>
<li class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">relation
names, e.g. colour vs has_colour vs colour_of<o:p></o:p></span></li>
<li class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">instance
names<o:p></o:p></span></li>
<li class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">the
name
of the ontology, its versions, namespaces and term IDs<o:p></o:p></span></li>
</ul>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">2.3</span></b><span
style="font-family: Arial;"> (If your answer to 2.1 is negative) Have
you
re-used existing naming conventions from other ontology groups?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example
have you applied the GO editor style guide or conventions from other
sources, e.g. ontology tutorials or guidelines from standardization
bodies such as
ISO?<o:p></o:p></span></p>
<h3 style="text-align: justify; line-height: 150%;"><u>3. Questions on
the
implementation of names<o:p></o:p></u></h3>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b><span
style="font-family: Arial;">3.1 </span></b><span
style="font-family: Arial;">Which of the following categories of names
(or
name types) do you record in your ontology and which one do you
anticipate
such common naming conventions are useful for?<i style=""><o:p></o:p></i></span></p>
<p class="ParawithChead" style="margin-top: 0cm; line-height: 150%;"><span
style="line-height: 150%; font-family: Arial;">Some examples are
provided below, add if required:<i style=""><o:p></o:p></i></span></p>
<p class="MsoNormal"
style="margin-left: 54pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 150%; font-family: Symbol;"><span
style="">·<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">preferred
name<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-left: 54pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 150%; font-family: Symbol;"><span
style="">·<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">short
name
or display name<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-left: 54pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 150%; font-family: Symbol;"><span
style="">·<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">formal
name<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-left: 54pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 150%; font-family: Symbol;"><span
style="">·<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">synonym<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-left: 54pt; text-align: justify; text-indent: -18pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 150%; font-family: Symbol;"><span
style="">·<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">foreign
language
translations<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin: 0cm 0cm 6pt 53.85pt; text-align: justify; text-indent: -17.85pt; line-height: 150%;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 150%; font-family: Symbol;"><span
style="">·<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">broader
or
narrower term<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b><span
style="font-family: Arial;">3.2</span></b><span
style="font-family: Arial;"> (If applicable) Which ontology language
idioms
do you use to capture the categories of names, listed in question 3.1?
Please,
provide examples.</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">In OWL
the
preferred class name are probably captured using the rdfs:label idiom
and
foreign language translation via another rdfs:label idiom with the lang
attribute
set. Synonyms are probably captured by some self-created OWL annotation
properties
or in OBO by the ‘exact_synonym’ idiom.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b><span
style="font-family: Arial;">3.3 </span></b><span
style="font-family: Arial;">Do you think there is a need to expand the
expressivity
of the ontology representation languages in order to provide more
naming
flexibility? What elements are missing?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b><span
style="font-family: Arial;">3.4</span></b><span
style="font-family: Arial;"> Did you use any features/functions of
your
ontology editor to check for consistency within the names?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">In
Protégé
these features would be the browser key, PROMPT or StringSearchTab, and
the
redundancy check functionality in OBO Edit. Specialized software tools
also
exist to check naming conventions, e.g. Validator (<a
href="http://www.kismeta.com/Validtr.html">http://www.kismeta.com/Validtr.html</a>)<o:p></o:p></span></p>
<h3 style="text-align: justify; line-height: 150%;"><u>4. In depth
questions
on specific naming conventions<o:p></o:p></u></h3>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.1 Explicit and concise
names
and context independence<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.1.1</span></b><span
style="font-family: Arial;"> Do you put any constraints on the use of
natural
language?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example,
do you omit nouns, articles or other words to ensure shorter names,
e.g. <i style="">‘two dimensional J-resolved’, </i>in place of <i
style="">‘the
two dimensional J-resolved pulse sequence’? </i><span style="">If yes,
please describe.</span><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.1.2</span></b><span
style="font-family: Arial;"> Do you make sure all the names are
understandable
on their own, even when viewed outside of the immediate context?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.2 Compound names<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b><span
style="font-family: Arial;">4.2.1</span></b><span
style="font-family: Arial;"> Do you apply any conventions that help
string
matching? For example, when creating compound names do you try to build
the
names out of already defined building blocks, re-using the same words
or
word-parts (affixes) present in other names and other representational
units?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example,
use ‘x_part_of_process’, ‘y_part_of_process’ and ‘z_part_of_process’
using
consistently the string ‘part of’ (used and defined elsewhere) instead
of
using also a synonymous strings e.g.<span style=""> </span>‘x_component_of_process’,
‘y_part_of_process’, ‘z_portion_of_process’, introducing heterogeneity.
GO
for example re-uses the string ‘development’ in such a defined way all
over in its class names.<o:p></o:p></span></p>
<p class="MsoBodyText" style=""> </p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.2.2</span></b><span
style="font-family: Arial;"> Do your names contain defined strings
that
have a special defined meaning in each occurrence?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"> </p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">Defined
strings
could indicate administrative metadata, e.g. as in the names ‘?device’
or
‘device refine’.</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"> </span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">GO
used
the ‘sensu’ string to constrain validity, e.g. species specificity as
in
‘fruiting body development (sensu Bacteria)’ (GO:0030583, Note that the
‘sensu’ practice is now discouraged in GO in favour of stating
appropriate differentia explicitly and avoiding the taxon in names and
definitions, e.g. ‘cell wall
(sensu bacteria)’ becomes ‘peptidoglycan-based cell wall’ ). </span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b><span
style="font-family: Arial;">4.2.3 </span></b><span
style="font-family: Arial;">Have you developed any guidelines to
create
compound names?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example
conventions that demand a specific order of types of words within the
name.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.3 Homonyms<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.3.1 </span></b><span
style="font-family: Arial;">How do you cope with homonyms and highly
ambiguous names?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example,
one can try to avoid or disambiguate homonyms like ‘set’, which can
indicate
a plurality as in ‘protocol set’, as well as an action as in ‘parameter
set’.
OpenCyc uses qualifiers as name suffixes to disambiguate homonyms, e.g.
‘Plant-the
factory’ vs. ‘Plant-the organism’.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.4 Consistency of language<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.4.1</span></b><span
style="font-family: Arial;"> Do you consistently apply British or US
English
word forms?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example
using ‘polymerising’ vs. ‘polymerizing’ throughout.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.4.2</span></b><span
style="font-family: Arial;"> Do you encounter cases where
inconsistency
arises from including words from different languages? If yes, please
explain
how you tackle these inconsistencies.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example,
‘gut’ is the English word for the Latin ‘intestine’<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.5 Noun and verb forms<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.5.1</span></b><span
style="font-family: Arial;"> Do you encode word forms consciously and
in
a consistent way within your names and do you have any guidelines
regarding
word forms?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example,
using ‘to be measured’ (future) and ‘measured’ (past) or the
time-neutral
noun form ‘measurement’ in certain circumstances only.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.6 Abbreviations and
acronyms<o:p></o:p></span></b></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.6.1 </span></b><span
style="font-family: Arial;">How do you handle acronyms and
abbreviations
and how do you deal with widely used acronyms, .e.g. ‘NMR’ that would
result
in very long name when resolved? Could a <i style="">cut-off</i> be
defined
when an acronym can be used in a name and still be intuitive and
understandable
throughout the domain?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.7 Singularity<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.7.1</span></b><span
style="font-family: Arial;"> Do you capture plural or singular word
forms
throughout your ontology? When capturing pluralities, do you use a
consistent naming convention?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example
one could restrict the usage of plurality indicators, e.g. either ‘Xs’
‘X
collection’, ‘X set’, or ‘aggregate of X’ throughout.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.8 Positive names<o:p></o:p></span></b></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.8.1 </span></b><span
style="font-family: Arial;">Do you apply negative names such as
‘non-separation
device’?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.8.2 </span></b><span
style="font-family: Arial;">Do you explicitly exclude things within
your
names?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example
in gene ontology one can find ‘</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"><a
href="http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0016812">hydrolase
activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic
amides</a>’ (<a
href="http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0016812">GO:0016812</a>).</span><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.9 Conjunctions<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.9.1</span></b><span
style="font-family: Arial;"> Do the names in your ontology contain
logical connectives and Boolean operators such as ‘or’ or ‘and’, e.g.
as in ‘strain
or line’ or </span><span style="font-family: Arial;">‘ <a
href="http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0002504">antigen
processing and presentation of peptide or polysaccharide antigen via
MHC class II</a>’ (<a
href="http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0002504">GO:0002504</a>)?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.9.2</span></b><span
style="font-family: Arial;"> Do the names in your ontology contain
hyphens, slashes, parenthesis or other symbols and if so, do you use
them consistently? If yes, please explain their meaning and use.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">In
many ontologies
currently the hyphen and slashes are used with different underlying
meanings.
Hyphens can indicate omissions in names (ellipse or apocope), e.g.
‘gene-technology’
for ‘gene modification technology’, indicate logical connectives, e.g.
‘black-white’,
or ranges, e.g. ‘10-100’.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.10 Taboo words<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.10.1</span></b><span
style="font-family: Arial;"> Do names in your ontology contain words
that
refer to the representational units (e.g. class or relation) they are
encoded in, rather than to what is represented<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example
as in ‘protocol class’, ‘animal type’, ‘color attribute’, ‘ligand
relation’.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.11 Typography</span></b><span
style="font-family: Arial;"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.11.1</span></b><span
style="font-family: Arial;"> Which typographical convention, e.g.
lower
case, UPPERCASE, mixed Case or CamelCase do you use for the categories
of names (listed in question 3.1)?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">Under
the
OBO umbrella one can find ‘MyClass’ ‘My Class’, ‘My-Class’, ‘My_Class’,
‘My_class’ and ‘my class’ conventions, even within one ontology and
throughout different representational idioms. In the AI community the
convention to have classes starting upper-case and relations and
instances starting lower-case is common.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.11.2</span></b><span
style="font-family: Arial;"> Do you use sub- or superscripts or other
text
formatting to encode additional information? <o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.11.3</span></b><span
style="font-family: Arial;"> Do you use any character as a word
separator
(such as ‘_’, ‘-‘, ‘ ‘, etc. ) within compound names? If yes, please,
explain the reason of your choice.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">For
example,
XML based languages, such as OWL, cannot have the space separator,
because they need to be a valid when part of URIs, where space is not
allowed. CamelCase
is problematic for text mining since indicators for word-borders are
lost in CamelCase.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.11.4</span></b><span
style="font-family: Arial;"> How do you handle chemical element
symbols,
Greek symbols like </span><strong><span
style="font-family: Symbol; font-weight: normal;"><span style="">a</span></span></strong><strong><span
style="font-family: Arial; font-weight: normal;">,</span></strong><b
style=""><span style="font-family: Arial;"> </span></b><span
style="font-family: Arial;">and other special characters like <strong><span
style="font-family: Arial; font-weight: normal;">° C</span></strong><strong><span
style="font-family: Arial;"> </span></strong>?<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><b
style=""><span style="font-family: Arial;">4.11.5</span></b><span
style="font-family: Arial;"> Do you have to handle product names or
registered brand names? If yes, how do you render their names intuitive
(or do you capture them as they are) ?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 6pt; text-align: justify; line-height: 150%;"><span
style="font-size: 10pt; line-height: 150%; font-family: Arial;">A
brand name
‘US 2’, describing an NMR magnet, could be renamed by using the company
name
as prefix, the product brand name as infix and the product type
(superclass)
as headword/suffix, e.g. use ‘Bruker US 2 NMR magnet’.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify; line-height: 150%;"><span
style="font-family: Arial;"><o:p> </o:p></span><br>
<b style=""><span style="font-family: Arial;">Lastly, is there any
final
comment you want to make, including additional questions that should
have
been in this questionnaire? Has every naming issue you came across been
covered?<o:p></o:p></span></b></p>
<b style=""><span style="font-family: Arial;">THANKS</span></b><br>
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