Transcript www.crossref.org

Technical Meeting
September 17, 2003
London
2003 CrossRef Annual Member Meeting
Technical Working Group
1
Agenda
9:00 - 9:05
Introduction
9:05 - 9:30
Review of system operation, configuration & issues
9:30 -10:00
TOC Syndication Using RSS Tony Hammond, Elsevier
10:00 - 10:15
Coffee Break
10:15 - 11:15
New system features
11:15 - 11:45
Related technology topics
11:45 - ?
Open discussion
2003 CrossRef Annual Member Meeting
Technical Working Group
2
Operational Issues

Current configuration and planned changes

System utilization / query response times

Conflicts

Schema Issues

Procedures

Misc. (special characters, getting XML, reports …)

Where to get help
2003 CrossRef Annual Member Meeting
Technical Working Group
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Current Configuration & Planned Changes
Java
10 Mb full dup
Dell 2650
Dell 2650
Dell 2650
•Web / synch queries
100 Mb switch
Database
Sun E450
4 480Mhz Sparc II
4GB Mem
•Batch processing
- deposits
- asynch queries

•Oracle 8.1.7
Planned changes

Replace the database machine with a faster Sun box and better disks

Add a load balancer (service) on the front end so the Web component can run
on more than one machine (good reason to switch to http://doi.crossref.org)

Add a shadow ethernet drop from the co-location facility
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Technical Working Group
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System Utilization

Operations

Availability (1/03 – 8/03): 97.6%

Performance : 1 successful query = avg. response time is 0.656 seconds
1 failed query = avg. response time is 1.2 seconds
Deposit performance depends on number of jobs in the Q (4 simultaneously)
(50% < 5min) (12%< 1hr) (16% < 6hr) (7%< 12hr) (10% < 24hr) (5% > 24hr)

System utilization driven by database use
Sat
Sun
2003 CrossRef Annual Member Meeting
Mon
Tue
Wed
Thu
Technical Working Group
Fri
5
System Utilization

Query response time
(1)
(2 to 9)
(10 to 24)
60
50
40
30
20
10
0
0
8
Sat
16
0
8
16
Sun
0
8
16
Mon
0
8
Tue
16
0
8
16
Wed
2003 CrossRef Annual Member Meeting
Technical Working Group
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8
Thu
16
0
8
16
Fri
6
System Utilization

Query response time
(25 to 49)
(50 to 99)
(100+)
1000
900
800
700
600
500
400
300
200
100
0
0
8
Sat
16
0
8
Sun
16
0
8
Mon
16
0
8
Tue
16
0
8
Wed
2003 CrossRef Annual Member Meeting
Technical Working Group
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0
8
Thu
16
0
8
16
Fri
7
Conflicts

A conflict is created when 2 (or more) DOIs are deposited with the
same metadata
Journal / Author / Volume / Issue / Page / Article Title / Sequence-Number

Happens when:
No page numbers available Ok
Limited meta-data (no author or article title) Ok
Same article title (‘Book Reviews’) on the same page (no author) Ok
Two publishers host the same article Bad
Publisher wants to assign a new DOI (naming convention change) Ok?

What can be done about them
 Re-deposit one of the DOIs and change the meta-data (auto-resolve)
 An administrator can erase the conflict (both DOIs remain as peers)
A meta-data search will yield no (ambiguous) results or multiple hits
 An administrator can make one the ‘prime’ and the other an ‘alias’
The ‘alias’ is essentially deleted, it can never be updated again
(unless we do an ‘un-do’)
2003 CrossRef Annual Member Meeting
Technical Working Group
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Conflicts

What you see in your log
<record_diagnostic status="Warning">
<doi>10.1046/j.1365-2141.2003.04548.x</doi>
<msg>Added with conflict</msg>
<conflict_id>44487</conflict_id>
<dois_in_conflict>
<doi>10.1046/j.1365-2141.2003.04528.x</doi>
</dois_in_conflict>
</record_diagnostic>
<batch_data>
<record_count>24</record_count>
<success_count>23</success_count>
<warning_count>1</warning_count>
<failure_count>0</failure_count>
</batch_data>
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Technical Working Group
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Conflicts

The conflict report (we email them now, soon to be available on www.crossref.org)
Conflict report for 10.1016 created on Jul 24,2003
===========================================
ConfID: 105
CauseID: 14902006
OtherID: 1711,
JT: Analytica Chimica Acta
MD: Louwerse, 346 ,3,285,1997,Monitoring time-varying concentrations in
sample streams by multiple input chromatography
DOI: 10.1016/S0003-2670(97)00138-4 (105-null )
DOI: 10.1016/S0003-2670(97)90065-9 (105-null )
===========================================
…
======== Number Of Conflicts: 25673 ========
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Conflicts

Un-resolved conflicts (as of July 24)
Prefix
Count
Prefix
Count
10.1006
10.1021
10.1103
10.1191
10.1111
10.1046
10.1079
10.1017
10.1054
10.1016
30
13
7
8
3
133
2
49
15
25673
10.1055
10.1109
10.1023
10.1097
10.1067
10.1038
10.1177
10.1007
10.1086
10.1053
1
18
81
2927
20
222
306
1
23
109
Prefix
2003 CrossRef Annual Member Meeting
Technical Working Group
10.1002
10.1034
10.5555
10.1057
10.1113
10.1211
10.1263
10.1076
10.1345
10.1350
10.1354
Count
300
9
1
64
1
1
66
20
1
1
20
11
Schema Issues

Versions
Currently at 2.0.5, several small changes have been made to bring
the schema to 2.0.5.3 (do not include the minor rev # in the
declarations)

<?xml version="1.0" encoding="UTF-8"?>
<doi_batch version="2.0.5"
xmlns="http://www.crossref.org/schema/2.0.5"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.crossref.org/schema/2.0.
5 http://www.crossref.org/schema/2.0.5/crossref.xsd">
<head>
When a major change occurs (like forward linking) the schema will
be revised and you must change the declaration to pick up the changes

(the system will recognize multiple schemas)
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Technical Working Group
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Schema Issues

Character entities


Schema does (generally) not do character entities
Xerces will understand certain basic Latin
&amp; &lt; &gt; &quot;

For others you must numerically encode them
Greek small letter alpha => &#945; or &#x3B1;
http://www.w3.org/TR/REC-html40/sgml/entities.html#h-24.2.1
http://www.unicode.org/
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Technical Working Group
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Schema Parser
http://www.crossref.org/06members/55InstructionsforNewSchema.html
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Technical Working Group
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Schema Parser
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Technical Working Group
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Procedures
 DOI Ownership Transfer
 When a journal is transferred between two publishers
1) Notify CrossRef via email, supply journal title, old and new prefix
2) Supply a list of DOIs (CrossRef can generate the list if needed)
3) Supply new URLs (if needed)
4) CrossRef processes transfer
- changes ownership in CrossRef MDDB
- changes administration in handle system
 DOI Changes & Conflict Resolution
 When a new DOI is to be assigned to replace another DOI
(due to error or the need to restructure the suffix composition)
1) Construct an XML deposit file for the new DOIs
(same metadata as the old DOIs)
2) Deposit it, examine the log for conflict warnings
3) Contact CrossRef so an administrator can ‘overwrite’ the old DOIs with
the new DOIs
- deprecates old DOI in MDDB
- aliases old DOI to new DOI in handle system
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Technical Working Group
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Schema Issues

Publishers Still Using the DTD
aamr
amerindhyg
amet
amonh
ams
apha
arnold
aspbs
biomedcen
brill
brps
cabi
cup
dekker
ediciones
elsevier
eurrespsoc
fdcomm
funinapr
geosociety
hhs
hhs-mosby
hindawi
ilsi
inschemeng
isas
jmry
karger
lawerl
librapharm
2003 CrossRef Annual Member Meeting
Technical Working Group
lww
maney
maryanne
mcb
mit
nature
pengp
pharmapress
ppress
roysocmed
sage
schweiz
sivb
springer
taylor
urfi
wiley
wscientific
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Special Characters
The query: |j phys B at mol opt phys||36||1129||||
In a Browser (IE 6.0)
13616455,09534075|Journal of Physics B Atomic Molecular and Optical
Physics|Tr bert|36|6|1129|2003|full_text||10.1088/0953-4075/36/6/305
In a DOS command window
13616455,09534075| Journal of Physics B Atomic Molecular and Optical Physics|
Trábert|36|6|1129|2003| full_text||10.108/53-4075/36/6/305
Byte string of the author’s name
Trábert: [0]=0x54,[1]=0x72,[2]=0xa0,[3]=0x62,[4]=0x65,[5]=0x72,[6]=0x7
What was deposited
<surname>Tr&#160;bert</surname> #160 = #xA0
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Special Characters
The query: |j phys org chem||16||213||||
In a Browser (IE 6.0)
10991395,08943230|Journal of Physical Organic
Chemistry|Ch ciDska|16|4|213|2003|full_text||10.1002/poc.596
In a DOS command window
10991395,08943230|Journal of Physical Organic Chemistry
|Ch↓ciDska|16|4|213|2003|full_text||10.1002/poc.596
Byte string of the author’s name
Ch↓ciDska: [0]=0x43,[1]=0x68,[2]=0x19,[3]=0x63,[4]=0x69,[5]=0x44,
[6]=0x73,[7]=0x6b,[8]=0x61
What was deposited
<surname>Ch&#x0119;ci&#x0144;ska</surname>
0x19 is unprintable, 0x44 is a ‘D’
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Technical Working Group
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Special Characters
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Special Characters
<?xml version = "1.0" encoding = "UTF-8"?>
<doi_batch version = "0.3">
…
<body>
<doi_record type = "full_text">
<doi_data>
<doi>10.1002/poc.596</doi>
<url/>
</doi_data>
<journal_article_metadata>
<article>
<author sequence = "first">
<given_name/>
<surname>Ch&#x0119;ci&#x0144;ska</surname>
</author>
<date type = "print">
<year>2003</year>
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Getting the XML for DOIs


In order to update meta-data you need to have the XML

An update is a complete re-write, omitted fields in the update are
removed from the database

The update can be in Schema even if the original deposit was in DTD
CrossRef can now retrieve the XML for a list of DOIs.

DOIs can be from different submissions

Extracted XML will be in the same format as the deposit/update

Email the list of DOIs to [email protected]
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Depositor Report
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Query Formulation
 Journal queries differ from Conference Proceedings and Book queries
Journals:
ISSN |TITLE/ABBREV | FIRST AUTHOR| VOLUME | ISSUE | START PAGE | YEAR | RESOURCE TYPE | KEY | DOI
Books and conference proceedings:
ISBN/ISSN | SER_TITLE | VOL_TITLE | AUTHOR/EDITOR | VOLUME | EDITION_NUMBER | PAGE | YEAR |
COMPONENT_NUMBER | RESOURCE_TYPE | KEY | DOI
For Conference Proceedings:
SER_TITLE =>
<conference><proceedings_metadata><series_metadata><titles><title>
(one, optional)
VOL_TITLE => <conference><proceedings_metadata><proceedings_title>
(must have one)
Note: < conference ><conference_paper><titles><title> is not searchable
For Books:
SER_TITLE => <book>><book_metadata><series_metadata><titles><title>
VOL_TITLE => <book><book_metadata><titles><title>
(1..6 of either of these)
Note: <book><content_item><titles><title> is not searchable
Note: For series titles to matter you must assign them a DOI when depositing
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Where to get help

How to get started
http://www.crossref.org/02publishers/23how_start.html

How to deposit
http://www.crossref.org/02publishers/24upload_spec.html

How to query
http://www.crossref.org/02publishers/25query_spec.html

System help pages (more technical)
http://doi.crossref.org/doc/userdoc.html
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RSS And TOCs
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New System Features

Tracking IDs

XML Query Format

Enhanced XML Results

Forward Matching

Forward Linking

Real Time Queries
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Tracking IDs

Problem: Deposit logs received via email is error prone

Solution: Allow depositors to interrogate the system

Using the batch ID you specify in the XML file
<doi_batch xmlns="http://www.crossref.org/schema/2.0.5" ...
<head>
<doi_batch_id>2003-08-11-1006001</doi_batch_id>
<timestamp>20030811104844000</timestamp>
<depositor>
<name>Dale Langley</name>

Perform an HTTP Get
http://doi.crossref.org/servlet/submissionDownload?usr=<USR>&
pwd=<PWD>&doi_batch_id=2003-08-11-1016008&type=result
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Tracking IDs
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XML Query Format

Problem: Piped queries can be awkward to deal with and not extensible

Solution: Create an XML schema for queries
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://www.crossref.org/qschema/1.0"
xmlns="http://www.crossref.org/qschema/1.0">
http://doi.crossref.org/doc/tech/crossref_query_input.xsd

To use some of the new CrossRef features you must query using this format
 Request multiple hits
 Request forward matching
 Turn off fuzzy matching (on a field by field basis)
 Use tracking Ids on query jobs
 Match on NULL fields
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Technical Working Group
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Enhanced XML Query Results

Problem: We wanted to supply more information about the query results

Solution: Create an extended XML schema for query results

The existing XML query result format is still available (no schema or DTD)
http://doi.crossref.org/doc/tech/crossref_query_output.xsd

Results in this format can show
 Multiple hits – when the metadata search resolved to more than one DOI
(ambiguous results produce NO match in a normal query)

Fuzzy matching indicators
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Enhanced XML Query Results
Input
Output
<?xml version="1.0" encoding="UTF-8" ?>
<?xml
version = version="1.0"
"1.0" encoding="UTF-8"?>
<crossref_result
xmlns="http://www.crossref.org/qschema/1.0"
<query_batch
version="1.0" xmlns = "http://www.crossref.org/qschema/1.0"
<query_result>
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<head>
<head>
<email_address>[email protected]</email_address>
<email_address>[email protected]</email_address>
<doi_batch_id>SomeTrackingID1</doi_batch_id>
<doi_batch_id>SomeTrackingID1</doi_batch_id>
</head>
</head>
<body>
<body>
<query key="MyKey1" status="resolved">
<query key="MyKey1" enable-multiple-hits="false">
<doi>10.1002/dvdy.10084</doi>
<journal_title>Develop. Dynamics</journal_title>
<issn>10970177</issn>
<author match="null"></author>
<journal_title
match="fuzzy">Developmental Dynamics</journal_title>
<volume>223</volume>
<volume
match="exact">223</volume>
<first_page>426</first_page>
<issue>3</issue>
<year>2002</year>
<first_page
match="exact">426</first_page>
</query>
<year
match="exact">2002</year>
</body>
<publication_type>full_text</publication_type>
</query_batch>
</query>
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Forward Matching

Problem: Members must re-query CrossRef to find DOIs from recent deposits

Solution: Create a stored query mechanism where CrossRef ‘remembers’ failed
queries, who sent them and notifies them when a deposit resolves them

Request forward matching in the query
<query key="MyKey1" enable-multiple-hits="false“
forward-match=“true”
key=“some-unique-key”>
<journal_title>Develop. Dynamics</journal_title>
<author match="null"></author>
<volume>223</volume>
<first_page>426</first_page>
<year>2002</year>
</query>
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Forward Matching

Each stored query is identified by user assigned attributes
 The query must be given a unique ‘key’
 The request must have a unique ‘batch-id’

Identical queries are stored once, multiple users may be associated with one query

When a stored query matches an email is sent with the XML results
(one email per query)

Users may ‘poll’ for stored queries that have matched
http://doi.crossref.org/servlet/downloadStoredQueries?
usr=<username>&pwd=<password>&
startDate=<startDate>&endDate=<endDate>
Start and end dates are inclusive. Must be formatted a yyyy-mm-dd
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Forward Matching

Processing Forward Matches
1.
Upon receipt the query (if it initially fails) is sorted based on title
2.
When deposits are made, titles trigger corresponding stored queries
3.
Batch job will be run nightly to process all triggered stored queries
4.
If the batch does not complete in the allowed window it will pick
up from where it left off in the next interval
5.
Weekend intervals will be longer than weekday intervals
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Forward Linking
 A new
service to be deployed by year end (pending board final approval)
 Allow
the retrieval of DOIs for articles that cite another article

Builds on existing CrossRef transactions

Publishers deposit metadata for their articles

Publishers query for the references in those articles to get DOIs

If CrossRef knows which references go with which articles we
can tell owners of the cited articles who ‘cites’ them
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Technical Working Group
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Forward Linking
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Forward Linking

Include the list of references with the article when registering the DOI
 Combine deposit and query into one step

Or, upload a list of references for an article
Example:
H:[email protected]
[source document DOI] tab [||||||||reference DOI]
[source document DOI] tab [issn|journal|author|volume|issue|page|year]
[source document DOI] tab [reference DOI]
…
Constraints:
• The source document DOI must exist in CrossRef prior to using this method.
• If the reference is supplied as a DOI, that DOI must exist in CrossRef
• For bulk loads no metadata query results will be returned.
• One cited reference per line
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Forward Linking

Forward links (aka. Cited-By lists) will be retrieved by a simple query

Send in the DOI of the target article (a new HTTP request)

Receive an extended set of meta-data (in an XML response)
for each of the citing articles
Name
Comment
Full Journal Title
Abbreviated Journal Title
ISSNs
More than 1
Journal DOI
Article Title
Contributors
Required element in schema deposits
All authors, given and surname up to a
max of 10 (when >10 list as et al)
Volume
Issue
Page
Page range
Article DOI
Article Identifier
<identifier> or <item_number>
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Technical Working Group
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Real Time Queries


Real time queries are done on-the fly

When a user clicks on a link

When the page is constructed for display
The current HTTP GET interface is being used by some for real time queries


No guaranteed level of service BUT for single queries 1 second response
Does place an un-intended load on the system
 A ‘premium’ query
service will be available that operates on a different interface

Better, more deterministic access to the CrossRef system

Less overhead than the synchronous HTTP GET interface

In testing now!
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Technical Working Group
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Related Technologies

The Handle System

Parameter Passing

Open URL

Local Link Servers

Multiple Resolution
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Technical Working Group
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The Handle System

What is it ?

A network accessible database for retrieving name-value pairs

A “hash” where the DOI is the key

A system built by CNRI and licensed for use by the IDF (DOI)
Important: DOI and Handle are not the same thing!
DOIs are “handles” which are intended to behave a certain way

How does DOI / CrossRef use it ?

CrossRef is a service to input and update the name-value pairs

http://dx.doi.org is a resolver that knows what we want to do with DOIs
For key=10.xxxx/yyyy retrieve the name-value pair called ‘URL’
and redirect to the value string (which should be a URL)

DOI could (and may someday) operate on any look-up mechanism
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The Handle System
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The Handle System
<timestamp>0004</timestamp>
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OpenURL and DOIs/CrossRef
OpenURL and DOI are complementary technologies

CrossRef helps solve the appropriate copy problem by
providing a ‘reverse’ DOI lookup (DOI in / meta-data out)
http://doi.crossref.org/servlet/query?
id=10.1006/jmbi.2000.4282&pid=<USR>:<PWD>

CrossRef offers an OpenURL 1.0 compliant resolver
http://doi.crossref.org/resolve?pid=<USR>:<PWD>&aulast=Maas LRM
&title= JOURNAL OF PHYSICAL OCEANOGRAPHY&volume=32
&issue=3 &spage=870&date=2002
(This resolver will redirect you to the target document)
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Technical Working Group
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What does an OpenURL look like
http://resolver.example.org?
• Add
referrer
fixed
Start the
withreferent
the
elements
BaseURL
url_ver=z39.88-2003
&url_ctx_fmt=ori:fmt:kev:mtx:ctx
Version
&rfr_id=ori:rfr:publisher.com
Declare
Identifier for referrer
ContextObject
&rft_id=ori:doi:10.1126/science.275.5304.1320
format
Add
the metadata
&rft_id=ori:pmid:9036860
elements
&rft_val_fmt=ori:fmt:kev:mtx:journal
&rft.genre=article
Declare the
&rft.atitle=IsolationOpenURL
of a common“Referrer”
receptor Include
Domain
of
metadata
format
identifiers
for …
referrer
Shows referent (rft) format
&rft.jtitle=Science
(fmt) is by value (val)
Indicates we are using key&rft.aulast=Bergelson
encoded-values
(kev) as actual
Substitute
&rft.auinit=J
defined in the “journal”
matrix
values
for
the item
…
(mtx)
in
the
registry.
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Technical Working Group
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A&I (Ovid) as link source
Link Source
Link Menu
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Technical Working Group
Link Target
47
OpenURL Linking: SFX & CrossRef
DOI
link
DOI
Server
References
http://dx.doi.org/
doi=10.1034/j.1399-0039.2000.560502.x
OpenURL
Aware
OpenURL
http://www.sfx.edu/?
doi=10.1034/j.1399-0039.2000.560502.x
Metadata
DOI
Server
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Multiple Resolution
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Multiple Resolution

Re Hosted journal (the appropriate copy problem)
1.
Publisher A produces and hosts a journal from 1999 through 2002
2.
Publisher B acquires the journal in 2003 and hosts all back issues

3.
Pre 2003 DOIs are transferred to publisher B and the URLs are
reset to publishers B’s
A customer subscribes to publisher A and wants to go there for pre2003 issues.

Journal available from more than one site (not a mirror)

Availability of alternative services (print, rights clearance …)

Supplemental material
Manifestations & Relations
2003 CrossRef Annual Member Meeting
Technical Working Group
50
Multiple Resolution – things to consider

Multiple resolution is not always desirable (probably most of the time)

In some contexts the link should behave as a single resolution

Implementation concerns

Impact on the publisher’s Web site must be small (display and behavior)

Resolution process first step (when the user clicks) must be fast

Large data transfers may not be practical (link updates)

Do not place too high a load on any single point (i.e. Handle)

Policy concerns

Access control (who can get on the MR lists for a item)

Action control (who decides when MR will be available to the user)

Quality control (who monitors ‘landing page’ behavior)
2003 CrossRef Annual Member Meeting
Technical Working Group
51
Multiple Resolution – what's next

CrossRef and Copyright Clearance Center have started
a prototype

A white paper to be released this fall

Define the operational issues

Define the governance issues

Present possible technical options

Construct a demonstration prototype

Not a fully functional solution
2003 CrossRef Annual Member Meeting
Technical Working Group
52
Multiple Resolution
The technical issues are surmountable
The political and business case issues
will be much more difficult
2003 CrossRef Annual Member Meeting
Technical Working Group
53
CrossRef
Technical Working Group
 Join the TWG !!!
Mailing list [email protected]
Mail list archives available on www.crossref.org
Monthly teleconferences
Planning an ‘in-person’ TWG for later this year
[email protected]
2003 CrossRef Annual Member Meeting
Technical Working Group
54