Topic 3: GUIDs for Taxon Names and Taxon Concepts - Maybe ...

Kennedy, Jessie J.Kennedy at NAPIER.AC.UK
Fri Nov 4 13:17:48 CET 2005


Dear All

 

Sorry for coming in so late into the discussion in this list - I have a
bit of catching up to do....but have been reading the listings on this
Topic with great interest and agreeing with much of what has been said
by everyone but still seeing misunderstandings or disagreements between
people on what we mean and what we should do which is inevitable given
that people have different reasons for wanting GUIDs etc.

 

To summarise my take on what's been said and if I misquote anyone please
forgive me and feel free to correct me....

 

I agree with Donald (and Rich) about needing Taxon_Name_GUIDs and
Taxon_Concept_GUIDs.

 

I agree with Donald that a shorthand to referring to a Taxon_Concept is
the combination of Taxon_Name and the Taxon_Publication. This is
slightly but importantly different to Rich here in that the publication
should be seen as a taxonomic publication (for another discussion
elsewhere) rather than any publication - i.e. not simply usage of a name
which could include an observation or identification - this
interpretation  opens up Taxonomic_Concepts too widely to cover
potential taxa rather than those which have been defined, described and
published in some scientific manner.)

 

I agree with the principle that GUIDs do not have to be issued from a
central repository BUT.... 

 

I do not agree that we should be issuing GUIDs for every taxonomic
record - be that for Taxonomic_Name or Taxonomic_Concept. There needs to
be some control - even if the control is self imposed.

 

I agree with Sally that we should have Nomenclators provide GUIDs for
Taxon_Names but would be more strict and say that these names should
have only one GUID and that the GUID should always resolve to exactly
the same name. So IPNI would be plant names, Index fugorum fungi names,
zoobank when available animal names etc. and that we should share the
resource of fixing this rather than duplicating effort (if I had any
resource to give;-) ) IPNI and IF wouldn't overlap in names.

 

I agree that anyone should be able to assign GUIDs but for their "own"
Taxonomic_Concepts, (so for example a provider like say Mammal species
of the world (or Bergey's manual for bacteria) which has well described
concepts, could issue GUIDs for all of the concepts they recognise and
other users of concepts could use their GUID in their database to record
observations etc if they agreed with their concept. If they didn't agree
with the MSW concept they could publish their own Taxonomic_Concept and
GUID and relate it to some MSW Taxonomic_Concept GUID) BUT....

 

I would argue that we should try to avoid generating GUIDs multiple
times for legacy concepts. For example, as mentioned by Rich the
original descriptions of names are original concepts - we wouldn't want
ITIS, GBIF, Species 2000, SEEK and whomever else creating different
GUIDS of their own to represent this concept if possible or we would
never move towards knowing we're talking about the same thing (- how
this might be managed is probably for another discussion topic).  

 

I agree with Rod to the extent that moving forward with a distributed
GUID publication system is easy where providers publish GUIDs for their
own digital objects BUT....

 

I don't think it's helpful or in the spirit of GUIDs to take a digital
object and republish it with another GUID without managing the
replication of the GUIDs for the object - which could effectively be
what happens if every data provider just issues GUIDs for the data they
hold which is effectively the same as what someone else has already
published. I think we do want to move towards reuse of GUIDs as much as
possible and therefore sharing of work and easier and more accurate data
integration. Also, what's the point of having millions of unique GUIDs
if I don't know which one to put in "my" database to represent the
Taxon_Name or Taxonomic_Concept I want to refer to? Rod would suggest
this be self selecting (use your favourite provider, or the one you're
told to - but I don't think it's that simple and doesn't get us towards
a good solution - unless the one you're told to use does it properly!)

 

I don't agree with Rod that we should do only purely nomenclatural
mappings - as for most of the projects I'm involved with and people I've
spoken to this will not solve their problems - we do need to know what
the name means. However nomenclatural mapping is useful and a part of
solving the overall problem.

 

I agree with Rod that GUIDs will not solve all our problems but if
managed and planned in a sensible way they will help us on our way to
solving the problem.

 

What providers of GUIDs need to decide is what they are providing a GUID
for - in our area is it a Taxon_Name, a Taxonomic_Concpet, a
Taxonomic_Observation, a Specimen, a Description (of a specimen or
Taxonomic_Concept), a Taxonomic_Publication or whatever. Each of these
things can probably refer to some to the other things and these should
be using GUIDs. 

For example if you're an ecologist you might record survey data and
issue- 

a GUID for a Taxonomic_Observation which contains 

a GUID to a Taxonomic_Concept which contains 

a GUID to a Taxonomic_Name which in turn will contain 

a GUID to a Specimen - the type specimen 

a GUID to a Taxonomic_Name maybe the basionym

a Description which in turn will contain 

GUIDs to the Specimen(s) or Taxonomic_Concept described

 

The ecologist may only want to know about their observation of the
Taxonomic_Concept and not concern themselves with the embedded detail.
So hopefully you'll see that we really want commonality in usage of
GUIDs as much as possible so I think we need to think a bit about how we
manage this - possibly another topic for discussion and certainly one
that GBIF could lead.

 

I agree with Rod the idea of a local GUID as being nonsensical - GUID
meaning Globally Unique Identifier. The issue is about global uniqueness
and resolvability which are separate things but related in this
discussion. And as Rod says about whether we mean the same thing. Now as
Rod says sorting out the name part is a huge step forward I think
sorting out the Concept part is a bigger step forward - but won't EVER
solve the issue of whether or not someone identified something properly
or whether they're thinking the same as me but if we have
Taxonomic_Concepts (with GUIDs) we're nearer to knowing what we mean.
Isn't this what the semantic web people are saying - you can't assume
that because the name is the same we're talking about the same
thing..... So I do believe we need Taxonomic_Concepts and
Taxonomic_Names and all we're trying to do is sort out the terminology
and semantics for what concepts of organisms exist or have existed in
the world.

 

Jessie

 

            

 

 

 

 

 

 

 

 

 

Prof. J B Kennedy

School of Computing 

Napier University

10 Colinton Road

Edinburgh

EH10 5DT

Tel: +44 (0)131 455 2772

Fax: +44 (0)131 455 2727

Email: j.kennedy at napier.ac.uk

WWW: http://www.soc.napier.ac.uk/jessie

 


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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear All<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sorry for coming in so late into the discussion in this list
&#8211; I have a bit of catching up to do&#8230;.but have been reading the
listings on this Topic with great interest and agreeing with much of what has
been said by everyone but still seeing misunderstandings or disagreements
between people on what we mean and what we should do which is inevitable given
that people have different reasons for wanting GUIDs etc.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>To summarise my take on what&#8217;s been said and if I
misquote anyone please forgive me and feel free to correct me&#8230;.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with Donald (and Rich) about needing Taxon_Name_GUIDs
and Taxon_Concept_GUIDs.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with Donald that a shorthand to referring to a Taxon_Concept
is the combination of Taxon_Name and the Taxon_Publication. This is slightly but
importantly different to Rich here in that the publication should be seen as a taxonomic
publication (for another discussion elsewhere) rather than any publication &#8211;
i.e. not simply usage of a name which could include an observation or
identification &#8211; this interpretation &nbsp;opens up Taxonomic_Concepts
too widely to cover potential taxa rather than those which have been defined, described
and published in some scientific manner.)<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with the principle that GUIDs do not have to be issued
from a central repository BUT&#8230;. <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I do not agree that we should be issuing GUIDs for every
taxonomic record &#8211; be that for Taxonomic_Name or Taxonomic_Concept. There
needs to be some control &#8211; even if the control is self imposed.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with Sally that we should have Nomenclators provide
GUIDs for Taxon_Names but would be more strict and say that these names should
have only one GUID and that the GUID should always resolve to exactly the same
name. So IPNI would be plant names, Index fugorum fungi names, zoobank when
available animal names etc. and that we should share the resource of fixing
this rather than duplicating effort (if I had any resource to give;-) ) IPNI
and IF wouldn&#8217;t overlap in names.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree that anyone should be able to assign GUIDs but for their
&#8220;<b><span style='font-weight:bold'>own</span></b>&#8221;
Taxonomic_Concepts, (so for example a provider like say Mammal species of the
world (or Bergey&#8217;s manual for bacteria) which has well described concepts,
could issue GUIDs for all of the concepts they recognise and other users of concepts
could use their GUID in their database to record observations etc if they
agreed with their concept. If they didn&#8217;t agree with the MSW concept they
could publish their own Taxonomic_Concept and GUID and relate it to some MSW Taxonomic_Concept
GUID) BUT&#8230;.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I would argue that we should try to avoid generating GUIDs
multiple times for legacy concepts. For example, as mentioned by Rich the
original descriptions of names are original concepts &#8211; we wouldn&#8217;t
want ITIS, GBIF, Species 2000, SEEK and whomever else creating different GUIDS
of their own to represent this concept if possible or we would never move towards
knowing we&#8217;re talking about the same thing (- how this might be managed
is probably for another discussion topic). &nbsp;<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with Rod to the extent that moving forward with a
distributed GUID publication system is easy where providers publish GUIDs for their
own digital objects BUT&#8230;.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I don&#8217;t think it&#8217;s helpful or in the spirit of
GUIDs to take a digital object and republish it with another GUID without
managing the replication of the GUIDs for the object &#8211; which could effectively
be what happens if every data provider just issues GUIDs for the data they hold
which is effectively the same as what someone else has already published. I
think we do want to move towards reuse of GUIDs as much as possible and therefore
sharing of work and easier and more accurate data integration. Also, what&#8217;s
the point of having millions of unique GUIDs if I don&#8217;t know which one to
put in &#8220;my&#8221; database to represent the Taxon_Name or Taxonomic_Concept
I want to refer to? Rod would suggest this be self selecting (use your
favourite provider, or the one you&#8217;re told to &#8211; but I don&#8217;t think
it&#8217;s that simple and doesn&#8217;t get us towards a good solution &#8211;
unless the one you&#8217;re told to use does it properly!)<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I don&#8217;t agree with Rod that we should do only purely
nomenclatural mappings &#8211; as for most of the projects I&#8217;m involved with
and people I&#8217;ve spoken to this will not solve their problems &#8211; we do
need to know what the name means. However nomenclatural mapping is useful and a
part of solving the overall problem.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with Rod that GUIDs will not solve all our problems
but if managed and planned in a sensible way they will help us on our way to
solving the problem.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>What providers of GUIDs need to decide is what they are
providing a GUID for &#8211; in our area is it a Taxon_Name, a
Taxonomic_Concpet, a Taxonomic_Observation, a Specimen, a Description (of a
specimen or Taxonomic_Concept), a Taxonomic_Publication or whatever. Each of
these things can probably refer to some to the other things and these should be
using GUIDs. <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>For example if you&#8217;re an ecologist you might record
survey data and issue- <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>a GUID for a Taxonomic_Observation which contains <o:p></o:p></span></font></p>

<p class=MsoNormal style='text-indent:36.0pt'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>a GUID to a Taxonomic_Concept which contains
<o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:36.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>a GUID to a
Taxonomic_Name which in turn will contain <o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:72.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>a GUID to a
Specimen &#8211; the type specimen <o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:72.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>a GUID to a
Taxonomic_Name maybe the basionym<o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:36.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>a Description which
in turn will contain <o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:72.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>GUIDs to the
Specimen(s) or Taxonomic_Concept described<o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:72.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>The ecologist may only want to know about their observation
of the Taxonomic_Concept and not concern themselves with the embedded detail. So
hopefully you&#8217;ll see that we really want commonality in usage of GUIDs as
much as possible so I think we need to think a bit about how we manage this &#8211;
possibly another topic for discussion and certainly one that GBIF could lead.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I agree with Rod the idea of a local GUID as being nonsensical
&#8211; GUID meaning Globally Unique Identifier. The issue is about global uniqueness
and resolvability which are separate things but related in this discussion. And
as Rod says about whether we mean the same thing. Now as Rod says sorting out
the name part is a huge step forward I think sorting out the Concept part is a
bigger step forward &#8211; but won&#8217;t EVER solve the issue of whether or
not someone identified something properly or whether they&#8217;re thinking the
same as me but if we have Taxonomic_Concepts (with GUIDs) we&#8217;re nearer to
knowing what we mean. Isn&#8217;t this what the semantic web people are saying &#8211;
you can&#8217;t assume that because the name is the same we&#8217;re talking
about the same thing&#8230;.. So I do believe we need Taxonomic_Concepts and Taxonomic_Names
and all we&#8217;re trying to do is sort out the terminology and semantics for
what concepts of organisms exist or have existed in the world.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Jessie<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:108.0pt;text-indent:36.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>&nbsp;<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Prof. J B Kennedy<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>School of Computing <o:p></o:p></span></font></p>

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  w:insDate="2005-11-04T11:52:00Z" w:endInsAuthor="jessie"
  w:endInsDate="2005-11-04T11:52:00Z"><st1:place w:st="on"><st1:PlaceName
   w:st="on">Napier</st1:PlaceName></ns0:PlaceName></st1:place> <ns0:PlaceType
  w:insAuthor="jessie" w:insDate="2005-11-04T11:52:00Z" w:endInsAuthor="jessie"
  w:endInsDate="2005-11-04T11:52:00Z"><st1:PlaceType w:st="on">University</st1:PlaceType></ns0:PlaceType></ns0:place><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><ns0:Street w:insAuthor="jessie"
 w:insDate="2005-11-04T11:52:00Z" w:endInsAuthor="jessie"
 w:endInsDate="2005-11-04T11:52:00Z"><ns0:address w:insAuthor="jessie"
  w:insDate="2005-11-04T11:52:00Z" w:endInsAuthor="jessie"
  w:endInsDate="2005-11-04T11:52:00Z">10 Colinton Road</ns0:address></ns0:Street><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><ns0:place w:insAuthor="jessie"
 w:insDate="2005-11-04T11:52:00Z" w:endInsAuthor="jessie"
 w:endInsDate="2005-11-04T11:52:00Z"><ns0:City w:insAuthor="jessie"
  w:insDate="2005-11-04T11:52:00Z" w:endInsAuthor="jessie"
  w:endInsDate="2005-11-04T11:52:00Z">Edinburgh</ns0:City></ns0:place><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>EH10 5DT<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Tel: +44 (0)131 455 2772<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Fax: +44 (0)131 455 2727<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Email: <a href="mailto:j.kennedy at napier.ac.uk">j.kennedy at napier.ac.uk</a><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>WWW: <a href="http://www.soc.napier.ac.uk/jessie">http://www.soc.napier.ac.uk/jessie</a></span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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