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Life Sciences Identifiers — All Issues

  • Acronym: LIS
  • Issues Count: 14
  • Description: All Issues
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Issues Descriptions

double colon

  • Key: LIS-8
  • Legacy Issue Number: 7565
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Section 8.1 (page 7) incorrectly states "The LSID declaration consists of the following parts, separated by
    double colons". This should read "single colon".

  • Reported: LIS 1.0b1 — Wed, 7 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Reference incorrectly lists W3C

  • Key: LIS-13
  • Legacy Issue Number: 7573
  • Status: closed  
  • Source: Anonymous
  • Summary:

    This is a small issue but it there is a mistake in the references:

    Issue: In Section B, reference 11 incorrectly has "(W3C)" where it should
    say "(WS-I)"
    Suggested Solution:
    Change "(W3C)" to "(WS-I)"

  • Reported: LIS 1.0b1 — Fri, 9 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    Change "(W3C)" to "(WS-I)"

  • Updated: Fri, 6 Mar 2015 20:58 GMT

'binary64' conformance claim

  • Key: LIS-12
  • Legacy Issue Number: 7572
  • Status: closed  
  • Source: Anonymous
  • Summary:

    Issue: Section 13.2.2.1 mentions that implementors can use "binary64"
    encoding. This should either say "base64" encoding since that is the more
    accepted name for the encoding. Also, it should be explicitly noted that
    doing so will reduce the interoperability of the implementation
    significantly and that the resulting implementation will not be WS-I
    compliant.
    Suggested solution:
    Either remove this claim now that the attachments WS-I profile is further
    along, or at least explicitly note that the resulting implementation will
    not be WS-I compliant and might not be interoperable. Also, "binary64"
    should be changed to "base64".

  • Reported: LIS 1.0b1 — Fri, 9 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Spec conformant to WS-I attachments draft

  • Key: LIS-11
  • Legacy Issue Number: 7571
  • Status: closed  
  • Source: Anonymous
  • Summary:

    Issue: The WS-I has released the draft of their attachments profile since
    the LSID spec was finalized. I have verified that the WSDLs are correct
    according to that draft profile. The spec should be updated to mention
    that it is correct with respect to those drafts rather than the 'preview'
    it currently states.
    Suggested solution:

    • Section 13.2: Change "and the previews of upcoming Basic
      Profile 1.1 [12] with support for binary attachments descriptions in
      WSDL."
      to read "and the WS-I Attachments Profile 1.0 Board Approval Draft
      [12]."
    • Update the reference in Section B number 12 to be:
      WS-I Attachments Profile 1.0 Board Approval Draft:
      http://ws-i.org/Profiles/AttachmentsProfile-1.0-2004-06-11.html
  • Reported: LIS 1.0b1 — Fri, 9 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

misleading wording

  • Key: LIS-6
  • Legacy Issue Number: 7389
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    There is a misleading wording "both examples..." in the descriprion of
    method 'getLSIDPatternFromList'. It should be clarified.

  • Reported: LIS 1.0b1 — Fri, 28 May 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Metadata ports are ambiguous in WSDL

  • Key: LIS-9
  • Legacy Issue Number: 7569
  • Status: closed  
  • Source: Anonymous
  • Summary:

    Problem : Metadata ports are ambiguous in WSDL:
    The spec allows duplicate metadata to be served by different WSDL ports as
    well as multiple ports that are not duplicates. However, the spec does not
    specify a way for the client to determine which ports are duplicates and
    which are true new metadata.

    Suggested Solution:
    Change the WSDL service name to reference a unique metadata instance, and
    all endpoint bindings contained in that service would be duplicates. This
    one to one mapping between a service name and metadata would basically
    group duplicate ports into individual services. By retrieving one port
    from all the services a client is guaranteed to receive all of the
    metadata without retrieving duplicate information. This standard practice
    would solve the problem and be in the confines of a valid WSLD schema.

  • Reported: LIS 1.0b1 — Thu, 8 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

incorrect abbreviation DDNS

  • Key: LIS-14
  • Legacy Issue Number: 7589
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The spec uses on two places incorrect abbreviation DDNS instead of
    DDDS. The suggested resolution is to change it to DDDS (in sections 2
    "Conformance" and 13.3. "Discovering...").

  • Reported: LIS 1.0b1 — Wed, 14 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Inconsistent capitalization in WSDL

  • Key: LIS-10
  • Legacy Issue Number: 7570
  • Status: closed  
  • Source: Anonymous
  • Summary:

    We have noticed a small issue with the WSDL for the LSID spec. Just a
    small inconsistency.

    Issue: Inconsistent capitalization of 'lsid' between the Assigning service
    WSDL and the rest of the WSDL.
    Suggested solution: Make following changes to LSIDAssigningPortType.wsdl

    • line 37 - change 'LSIDList' to 'lsidList'
    • line 39 - change 'LSID' to 'lsid'
    • line 43 - change 'LSIDPatternList' to 'lsidPatternList'
    • line 45 - change 'LSIDPattern' to 'lsidPattern'
    • line 77 - change 'LSID' to 'lsid'
    • line 82 - change 'LSIDList' to 'lsidList'
    • line 85 - change 'LSID' to 'lsid'
    • line 94 - change 'LSIDPattern' to 'lsidPattern'
    • line 99 - change 'LSIDPatternList' to 'lsidPatternList'
    • line 102 - change 'LSIDPattern' to 'lsidPattern'
    • line 109 - change 'LSID' to 'lsid'
  • Reported: LIS 1.0b1 — Fri, 9 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

p.13, last sentence (

  • Key: LIS-7
  • Legacy Issue Number: 7563
  • Status: closed  
  • Source: Cambridge Semantics, Inc. ( Sean Martin)
  • Summary:

    On p.13, last sentence (Sect 10, LSID resolution discovery service): "Section 8.3 details an example of one such implementation using DDDS/DNS". This should read "Section 13.3"... (not 8.3)

  • Reported: LIS 1.0b1 — Tue, 6 Jul 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

how to use/implement LSIDs on top of existing databases

  • Key: LIS-5
  • Legacy Issue Number: 7388
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    It would be useful if the spec clarifies in text how to use/implement
    LSIDs on top of existing databases without changing their internal
    schemata.

  • Reported: LIS 1.0b1 — Fri, 28 May 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Regarding Life Sciences ID service lifesci 3-5-12, and3-12-02

  • Key: LIS-1
  • Legacy Issue Number: 6957
  • Status: closed  
  • Source: Fujitsu ( Tom Rutt)
  • Summary:

    This OMG spec specifies a mapping to Web services in section 8.2.

    The second para of 8.2 needs to be clarified to state that only the soap/http binding is conformant to the WS-I Basic ­Profile 1.0a. The basic profile has placed HTTP get/ mappings outside the scope (i.e., BP 1.0 conformant systems may ignore these bindings).

    This Lifesciencs mapping specifies and uses a new WSDL binding extension, FTP binding.

    It needs to be clarified that this is an extension to wsdl defined in this OMG spec, and needs to use an OMG lifesciences url (instead of an IBM url) for the namespace of the FTP finding extensions. The actual extension elements need to be defined in a schema which is part of this specification.

    The semantics of this new FTP binding do not seem toe be completely specified.
    The explanation of the FTP binding (8.2.4.3 Bindings for FTP) should be enhanced.

    In particular, it is unclear how the get data with range operation is mapped to FTP, since it states that the binding ignores the input message parts

  • Reported: LIS 1.0b1 — Thu, 5 Feb 2004 05:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Some WSDL files use names 'ibm'

  • Key: LIS-4
  • Legacy Issue Number: 7387
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Some WSDL files use names 'ibm'. This should be resolved to the 'omg',
    or similar.

  • Reported: LIS 1.0b1 — Fri, 28 May 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

compliance point is not clear

  • Key: LIS-2
  • Legacy Issue Number: 7385
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The compliance point is not clear. It should be stated clearly that
    implementing only one PSM is enough to become compliant with the spec.
    Also the text there saying "In some places the specification allows, after
    giving a proper reasoning, more freedom." should be more specific about
    which places are meant.

  • Reported: LIS 1.0b1 — Fri, 28 May 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Metadata_document and Timestamp definitions missing

  • Key: LIS-3
  • Legacy Issue Number: 7386
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    In PIM, there should be definitions (probably String) for the
    Metadata_document and Timestamp.

  • Reported: LIS 1.0b1 — Fri, 28 May 2004 04:00 GMT
  • Disposition: Resolved — LIS 1.0
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT