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<i>This is a reminder to our previous email, see below. Please try to
respond before 4th of September. Filling out the questionnaire will
take under an hour.</i><br>
<br>
Dear Plant Ontology curators.<br>
<i><br>
</i>This email is being sent at the request of the OBO Foundry
coordinators
Barry Smith, Suzi Lewis, Chris Mungall and Michael Ashburner.<br>
<br>
I am approaching you as an editors of the plant growth and development
stage ontology and would appreciate your input to
our survey on your current practice in
naming (labeling) entities within your ontology or controlled
vocabulary.<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 it out and send it back to me, or alternatively let me
know if an ontology editor is available for a phone or skype interview.<br>
<br>
Thanks in advance for your reply! <br>
<br>
Best regards, <br>
Daniel Schober<br>
<br>
<u> PS: <br>
</u>Note that the survey will be closed by September 7th and result
posted
at the wiki page.<br>
If you have any question, please don’t hesitate to contact me (<a
class="moz-txt-link-abbreviated" href="mailto:mcsuarez@fi.upm.es">schober@ebi.ac.uk</a>).<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>
<br>
<br>
<pre class="moz-signature" cols="72">--
__________________________________________________________________________________________
Dr. Daniel Schober
NET Project - Ontologist
The European Bioinformatics Institute email: <a
class="moz-txt-link-abbreviated" href="mailto:schober@ebi.ac.uk">schober@ebi.ac.uk</a>
EMBL Outstation - Hinxton direct: +44 (0)1223 494410
Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK Room: A3-141 (extension building)
Project page: <a class="moz-txt-link-abbreviated"
href="http://www.ebi.ac.uk/net-project">www.ebi.ac.uk/net-project</a>
Personal page: <a class="moz-txt-link-freetext"
href="http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734">http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734</a>
Former home page: <a class="moz-txt-link-freetext"
href="http://www.bioinf.mdc-berlin.de/%7Eschober/">http://www.bioinf.mdc-berlin.de/%7Eschober/</a>
</pre>
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