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<a class="uk-position-absolute uk-transform-center uk-padding" style="left: 76%; top: 32%"
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<a class="uk-position-absolute uk-transform-center uk-padding" style="left: 75%; top: 35%;"
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(click)="changeTab(4)" routerLink="/about" fragment="tabs_card"
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<a class="uk-position-absolute uk-transform-center uk-padding" style="left: 76%; top: 72%"
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<a class="uk-position-absolute uk-transform-center uk-padding" style="left: 75%; top: 72%"
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(click)="changeTab(5)" routerLink="/about" fragment="tabs_card"
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<li><a>Indexing</a></li>
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<li><a>Stats Analysis</a></li>
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</ul>
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<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
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src="assets/graph-assets/about/architecture/aggregation.png" alt="Aggregation">
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[class]="'uk-margin-bottom uk-margin-medium-right '+(aggregationReadMore ? '' : 'lines-18 multi-line-ellipsis')">
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<div class="uk-margin-bottom uk-margin-medium-right uk-text-small lines-18"
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[class.multi-line-ellipsis]="!aggregationReadMore">
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<div>
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OpenAIRE collects metadata records from a variety of content providers as described in
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<a href="https://www.openaire.eu/aggregation-and-content-provision-workflows" target="_blank">https://www.openaire.eu/aggregation-and-content-provision-workflows</a>.
|
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OpenAIRE aggregates metadata records describing objects of the research life-cycle from content
|
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providers compliant to the
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<a href="https://guidelines.openaire.eu" target="_blank">OpenAIRE guidelines</a>
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and from entity registries (i.e. data sources offering authoritative lists of entities, like OpenDOAR,
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and from entity registries (i.e. data sources offering authoritative lists of entities, like
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OpenDOAR,
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re3data, DOAJ, and funder databases).
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After collection, metadata are transformed according to the OpenAIRE internal metadata model, which is
|
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After collection, metadata are transformed according to the OpenAIRE internal metadata model, which
|
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is
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used to generate the final OpenAIRE Research Graph that you can access from the OpenAIRE portal and
|
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the
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APIs.
|
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<br><br>
|
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The transformation process includes the application of cleaning functions whose goal is to ensure that
|
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The transformation process includes the application of cleaning functions whose goal is to ensure
|
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that
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values are harmonised according to a common format (e.g. dates as YYYY-MM-dd) and, whenever
|
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applicable,
|
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to a common controlled vocabulary.
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The controlled vocabularies used for cleansing are accessible at
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<a href="http://api.openaire.eu/vocabularies" target="_blank">http://api.openaire.eu/vocabularies</a>.
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<a href="http://api.openaire.eu/vocabularies"
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target="_blank">http://api.openaire.eu/vocabularies</a>.
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Each vocabulary features a set of controlled terms, each with one code, one label, and a set of
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synonyms.
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If a synonym is found as field value, the value is updated with the corresponding term.
|
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Also, the OpenAIRE Research Graph is extended with other relevant scholarly communication sources that
|
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are too big to be integrated via the “normal” aggregation mechanism: DOIBoost (which merges Crossref,
|
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ORCID, Microsoft Academic Graph, and Unpaywall), and ScholeXplorer, one of the Scholix hubs offering a
|
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Also, the OpenAIRE Research Graph is extended with other relevant scholarly communication sources
|
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that
|
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are too big to be integrated via the “normal” aggregation mechanism: DOIBoost (which merges
|
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Crossref,
|
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ORCID, Microsoft Academic Graph, and Unpaywall), and ScholeXplorer, one of the Scholix hubs offering
|
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a
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large set of links between research literature and data.
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</div>
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<div *ngIf="!aggregationReadMore" class="uk-text-center clickable">
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<a (click)="aggregationReadMore = true" class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
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</div>
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</li>
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<li>
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<div class="uk-grid">
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<div class="uk-margin-bottom uk-text-small">
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<ul class="uk-subnav button-tab" uk-switcher>
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<li><a>Clustering</a></li>
|
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<li><a>Matching & Election</a></li>
|
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</ul>
|
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|
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<ul class="uk-switcher uk-margin align-list">
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<li>
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<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
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src="assets/graph-assets/about/architecture/deduplication.svg" alt="Deduplication">
|
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<div
|
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[class]="'uk-margin-bottom uk-margin-medium-right uk-text-small '+(dedupClusteringReadMore ? '' : 'lines-18 multi-line-ellipsis')">
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<div class="uk-margin-bottom uk-margin-medium-right uk-text-small lines-18"
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[class.multi-line-ellipsis]="!dedupClusteringReadMore">
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<div>
|
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<div>
|
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|
Clustering is a common heuristics used to overcome the N x N complexity required to match all
|
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Clustering is a common heuristics used to overcome the N x N complexity required to match
|
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all
|
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pairs of objects to identify the equivalent ones.
|
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|
The challenge is to identify a clustering function that maximizes the chance of comparing only
|
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The challenge is to identify a clustering function that maximizes the chance of comparing
|
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only
|
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records that may lead to a match, while minimizing the number of records that will not be
|
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195 |
matched while being equivalent.
|
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Since the equivalence function is to some level tolerant to minimal errors (e.g. switching of
|
|
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Since the equivalence function is to some level tolerant to minimal errors (e.g. switching
|
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of
|
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198 |
characters in the title, or minimal difference in letters), we need this function to be not
|
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too
|
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precise (e.g. a hash of the title), but also not too flexible (e.g. random ngrams of the
|
... | ... | |
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different versions and no clustering function will ever bring them into the same cluster.
|
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To match these requirements OpenAIRE clustering for products works with two functions:
|
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</div>
|
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|
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<ul class="portal-circle">
|
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<li>
|
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<div>DOI: the function generates the DOI when this is provided as part of the record
|
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233 |
229 |
</ul>
|
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<div>
|
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To give an idea, this configuration generates around 77Mi blocks, which we limited to 200
|
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|
records each (only 15K blocks are affected by the cut), and entails 260Bi matches. Matches in
|
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records each (only 15K blocks are affected by the cut), and entails 260Bi matches. Matches
|
|
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in
|
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a
|
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block are performed using a “sliding window” set to 80 records. The records are sorted
|
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lexicographically on a normalized version of their titles. The 1st record is matched against
|
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239 |
</div>
|
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</div>
|
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</div>
|
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<div *ngIf="!dedupClusteringReadMore" class="uk-width-3-5@m uk-text-center clickable"
|
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(click)="dedupClusteringReadMore = true">
|
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<a class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
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<div *ngIf="!dedupClusteringReadMore" class="uk-text-center clickable">
|
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|
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<a (click)="dedupClusteringReadMore = true" class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
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</div>
|
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<div *ngIf="dedupClusteringReadMore" class="uk-width-3-5@m uk-text-center clickable"
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(click)="dedupClusteringReadMore = false">
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<a class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
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<div *ngIf="dedupClusteringReadMore" class="uk-text-center clickable">
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<a (click)="dedupClusteringReadMore = false;" routerLink="./" fragment="tabs_card" class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
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</div>
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</li>
|
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<li>
|
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<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
|
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252 |
src="assets/graph-assets/about/architecture/deduplication.svg" alt="Deduplication">
|
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|
<div
|
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|
[class]="'uk-margin-bottom uk-margin-medium-right uk-text-small '+(dedupMatchingAndElectionReadMore ? '' : 'lines-18 multi-line-ellipsis')">
|
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<div class="uk-margin-bottom uk-margin-medium-right uk-text-small lines-18"
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[class.multi-line-ellipsis]="!dedupMatchingAndElectionReadMore">
|
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<div>
|
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<div>
|
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257 |
Once the clusters have been built, the algorithm proceeds with the comparisons.
|
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305 |
301 |
The titles of the two records are normalised and compared for similarity by applying
|
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302 |
the
|
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303 |
Levenstein distance algorithm.
|
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|
The algorithm returns a number in the range [0,1], where 0 means “very different” and
|
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The algorithm returns a number in the range [0,1], where 0 means “very different”
|
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and
|
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1
|
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means “equal”.
|
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308 |
If the distance is greater than or equal 0,99 the two records are identified as
|
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311 |
</li>
|
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<li>
|
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<div>Dates are not regarded for equivalence matching because different versions of the
|
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|
same records should be merged and may be published on different dates, e.g. pre-print
|
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same records should be merged and may be published on different dates, e.g.
|
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pre-print
|
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and published version of an article.
|
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</div>
|
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</li>
|
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</li>
|
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</ul>
|
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<div>
|
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|
Once the equivalence relationships between pairs of records are set, the groups of equivalent
|
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Once the equivalence relationships between pairs of records are set, the groups of
|
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324 |
equivalent
|
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325 |
records are obtained (transitive closure, i.e. “mesh”).
|
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|
From such sets a new representative object is obtained, which inherits all properties from the
|
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From such sets a new representative object is obtained, which inherits all properties from
|
|
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the
|
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merged records and keeps track of their provenance.
|
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329 |
The ID of the record is obtained by appending the prefix “dedup_” to the MD5 of the first ID
|
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330 |
(given their lexicographical ordering).
|
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</div>
|
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</div>
|
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</div>
|
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<div *ngIf="!dedupMatchingAndElectionReadMore" class="uk-width-3-5@m uk-text-center clickable"
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(click)="dedupMatchingAndElectionReadMore = true">
|
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|
<a class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
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<div *ngIf="!dedupMatchingAndElectionReadMore" class="uk-text-center clickable">
|
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<a (click)="dedupMatchingAndElectionReadMore = true" class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
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</div>
|
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<div *ngIf="dedupMatchingAndElectionReadMore" class="uk-width-3-5@m uk-text-center clickable"
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(click)="dedupMatchingAndElectionReadMore = false">
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<a class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
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<div *ngIf="dedupMatchingAndElectionReadMore" class="uk-text-center clickable">
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<a (click)="dedupMatchingAndElectionReadMore = false" routerLink="./" fragment="tabs_card" class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
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</div>
|
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</li>
|
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</ul>
|
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</div>
|
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|
<!-- </div>-->
|
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|
<!-- <div class="uk-width-expand">-->
|
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|
<!-- <img src="assets/graph-assets/about/architecture/deduplication.svg">-->
|
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|
<!-- </div>-->
|
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|
</div>
|
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</li>
|
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<li>
|
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|
<div class="uk-grid">
|
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|
<!-- <div class="uk-width-3-5@m">-->
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<div class="uk-margin-bottom uk-margin-medium-right uk-text-small">
|
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<div class="uk-margin-bottom uk-text-small">
|
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349 |
<ul class="uk-subnav button-tab uk-grid uk-grid-small" uk-switcher>
|
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|
<li><a>General</a></li>
|
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350 |
<li><a>Mining</a></li>
|
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351 |
<li><a>Bulk tagging/ Deduction</a></li>
|
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352 |
<li><a>Propagation</a></li>
|
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353 |
</ul>
|
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|
|
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354 |
<ul class="uk-switcher uk-margin">
|
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355 |
<li>
|
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356 |
<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
|
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357 |
src="assets/graph-assets/about/architecture/enrichment.svg" alt="Enrichment">
|
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|
<div class="uk-margin-bottom uk-margin-medium-right uk-text-small">
|
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|
<p>
|
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|
The aggregation processes are continuously running and apply vocabularies as they are in a given
|
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|
moment of time.
|
373 |
|
It could be the case that a vocabulary changes after the aggregation of one data source has
|
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|
finished,
|
375 |
|
thus the aggregated content does not reflect the current status of the controlled vocabularies.
|
|
358 |
<div class="uk-margin-bottom uk-margin-medium-right uk-text-small lines-18"
|
|
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[class.multi-line-ellipsis]="!enrichmentMiningReadMore">
|
|
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<div>
|
|
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The OpenAIRE Research Graph is enriched by links mined by OpenAIRE’s full-text mining
|
|
362 |
algorithms
|
|
363 |
that scan the plaintexts of publications for funding information, references to datasets,
|
|
364 |
software URIs, accession numbers of bioetities, and EPO patent mentions.
|
|
365 |
Custom mining modules also link research objects to specific research communities, initiatives
|
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366 |
and infrastructures.
|
|
367 |
In addition, other inference modules provide content-based document classification, document
|
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368 |
similarity, citation matching, and author affiliation matching.
|
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369 |
<br><br>
|
377 |
|
In addition, the integration of ScholeXplorer and DOIBooost and some enrichment processes
|
378 |
|
applied
|
379 |
|
on the raw
|
380 |
|
and on the de-duplicated graph may introduce values that do not comply with the current status
|
381 |
|
of
|
382 |
|
the OpenAIRE controlled vocabularies.
|
383 |
|
For these reasons, we included a final step of cleansing at the end of the workflow
|
384 |
|
materialisation.
|
385 |
|
The output of the final cleansing step is the final version of the OpenAIRE Research Graph.
|
386 |
|
</p>
|
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|
</div>
|
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|
</li>
|
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|
<li>
|
390 |
|
<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
|
391 |
|
src="assets/graph-assets/about/architecture/enrichment.svg" alt="Enrichment">
|
392 |
|
<div
|
393 |
|
[class]="'uk-margin-bottom uk-margin-medium-right uk-text-small '+(enrichmentMiningReadMore ? '' : 'lines-18 multi-line-ellipsis')">
|
394 |
|
<div>
|
395 |
|
<div>
|
396 |
|
The OpenAIRE Research Graph is enriched by links mined by OpenAIRE’s full-text mining
|
397 |
|
algorithms
|
398 |
|
that scan the plaintexts of publications for funding information, references to datasets,
|
399 |
|
software URIs, accession numbers of bioetities, and EPO patent mentions.
|
400 |
|
Custom mining modules also link research objects to specific research communities, initiatives
|
401 |
|
and infrastructures.
|
402 |
|
In addition, other inference modules provide content-based document classification, document
|
403 |
|
similarity, citation matching, and author affiliation matching.
|
404 |
|
<br><br>
|
405 |
|
<span class="portal-color">Project mining</span>
|
406 |
|
in OpenAIRE text mines the full-texts of publications in order to extract matches to funding
|
407 |
|
project codes/IDs.
|
408 |
|
The mining algorithm works by utilising
|
409 |
|
(i) the grant identifier, and
|
410 |
|
(ii) the project acronym (if available) of each project.
|
411 |
|
The mining algorithm:
|
412 |
|
(1) Preprocesses/normalizes the full-texts using several functions, which depend on the
|
413 |
|
characteristics of each funder (i.e., the format of the grant identifiers), such as stopword
|
414 |
|
and/or punctuation removal, tokenization, stemming, converting to lowercase; then
|
415 |
|
(2) String matching of grant identifiers against the normalized text is done using database
|
416 |
|
techniques; and
|
417 |
|
(3) The results are validated and cleaned using the context near the match by looking at the
|
418 |
|
context around the matched ID for relevant metadata and positive or negative words/phrases, in
|
419 |
|
order to calculate a confidence value for each publication-->project link.
|
420 |
|
A confidence threshold is set to optimise high accuracy while minimising false positives, such
|
421 |
|
as matches with page or report numbers, post/zip codes, parts of telephone numbers, DOIs or
|
422 |
|
URLs, accession numbers.
|
423 |
|
The algorithm also applies rules for disambiguating results, as different funders can share
|
424 |
|
identical project IDs; for example, grant number 633172 could refer to H2020 project EuroMix
|
425 |
|
but
|
426 |
|
also to Australian-funded NHMRC project “Brain activity (EEG) analysis and brain imaging
|
427 |
|
techniques to measure the neurobiological effects of sleep apnea”.
|
428 |
|
Project mining works very well and was the first Text & Data Mining (TDM) service of OpenAIRE.
|
429 |
|
Performance results vary from funder to funder but precision is higher than 98% for all
|
430 |
|
funders
|
431 |
|
and 99.5% for EC projects.
|
432 |
|
Recall is higher than 95% (99% for EC projects), when projects are properly acknowledged using
|
433 |
|
project/grant IDs.
|
434 |
|
<br><br>
|
435 |
|
<span class="portal-color">Dataset extraction</span>
|
436 |
|
runs on publications full-texts as described in “High pass text-filtering for Citation
|
437 |
|
matching”, TPDL 2017[1].
|
438 |
|
In particular, we search for citations to datasets using their DOIs, titles and other metadata
|
439 |
|
(i.e., dates, creator names, publishers, etc.).
|
440 |
|
We extract parts of the text which look like citations and search for datasets using database
|
441 |
|
join and pattern matching techniques.
|
442 |
|
Based on the experiments described in the paper, precision of the dataset extraction module is
|
443 |
|
98.5% and recall is 97.4% but it is also probably overestimated since it does not take into
|
444 |
|
account corruptions that may take place during pdf to text extraction.
|
445 |
|
It is calculated on the extracted full-texts of small samples from PubMed and arXiv.
|
446 |
|
<br><br>
|
447 |
|
<span class="portal-color">Software extraction</span>
|
448 |
|
runs also on parts of the text which look like citations.
|
449 |
|
We search the citations for links to software in open software repositories, specifically
|
450 |
|
github, sourceforge, bitbucket and the google code archive.
|
451 |
|
After that, we search for links that are included in Software Heritage (SH,
|
452 |
|
https://www.softwareheritage.org) and return the permanent URL that SH provides for each
|
453 |
|
software project.
|
454 |
|
We also enrich this content with user names, titles and descriptions of the software projects
|
455 |
|
using web mining techniques.
|
456 |
|
Since software mining is based on URL matching, our precision is 100% (we return a software
|
457 |
|
link
|
458 |
|
only if we find it in the text and there is no need to disambiguate).
|
459 |
|
As for recall rate, this is not calculable for this mining task.
|
460 |
|
Although we apply all the necessary normalizations to the URLs in order to overcome usual
|
461 |
|
issues
|
462 |
|
(e.g., http or https, existence of www or not, lower/upper case), we do not calculate cases
|
463 |
|
where a software is mentioned using its name and not by a link from the supported software
|
464 |
|
repositories.
|
465 |
|
<br><br>
|
466 |
|
<span class="portal-color">For the extraction of bio-entities</span>, we focus on Protein Data
|
467 |
|
Bank (PDB) entries.
|
468 |
|
We have downloaded the database with PDB codes and we update it regularly.
|
469 |
|
We search through the whole publication’s full-text for references to PDB codes.
|
470 |
|
We apply disambiguation rules (e.g., there are PDB codes that are the same as antibody codes
|
471 |
|
or
|
472 |
|
other issues) so that we return valid results.
|
473 |
|
Current precision is 98%.
|
474 |
|
Although it's risky to mention recall rates since these are usually overestimated, we have
|
475 |
|
calculated a recall rate of 98% using small samples from pubmed publications.
|
476 |
|
Moreover, our technique is able to identify about 30% more links to proteins than the ones
|
477 |
|
that
|
478 |
|
are tagged in Pubmed xmls.
|
479 |
|
<br><br>
|
480 |
|
<span class="portal-color">Other text-mining modules</span> include mining for links to EPO
|
481 |
|
patents, or custom mining modules for linking research objects to specific research
|
482 |
|
communities,
|
483 |
|
initiatives and infrastructures, e.g. COVID-19 mining module.
|
484 |
|
Apart from text-mining modules, OpenAIRE also provides a document classification service that
|
485 |
|
employs analysis of free text stemming from the abstracts of the publications.
|
486 |
|
The purpose of applying a document classification module is to assign a scientific text one or
|
487 |
|
more predefined content classes.
|
488 |
|
In OpenAIRE, the currently used taxonomies are arXiv, MeSH (Medical Subject Headings), ACM and
|
489 |
|
DDC (Dewey Decimal Classification, or Dewey Decimal System).
|
490 |
|
<br><br>
|
491 |
|
<hr>
|
492 |
|
[1] Foufoulas, Y., Stamatogiannakis, L., Dimitropoulos, H., & Ioannidis, Y. (2017, September).
|
493 |
|
High-Pass Text Filtering for Citation Matching.
|
494 |
|
In International Conference on Theory and Practice of Digital Libraries (pp. 355-366).
|
495 |
|
Springer,
|
496 |
|
Cham.
|
497 |
|
</div>
|
|
370 |
<span class="portal-color">Project mining</span>
|
|
371 |
in OpenAIRE text mines the full-texts of publications in order to extract matches to funding
|
|
372 |
project codes/IDs.
|
|
373 |
The mining algorithm works by utilising
|
|
374 |
(i) the grant identifier, and
|
|
375 |
(ii) the project acronym (if available) of each project.
|
|
376 |
The mining algorithm:
|
|
377 |
(1) Preprocesses/normalizes the full-texts using several functions, which depend on the
|
|
378 |
characteristics of each funder (i.e., the format of the grant identifiers), such as stopword
|
|
379 |
and/or punctuation removal, tokenization, stemming, converting to lowercase; then
|
|
380 |
(2) String matching of grant identifiers against the normalized text is done using database
|
|
381 |
techniques; and
|
|
382 |
(3) The results are validated and cleaned using the context near the match by looking at the
|
|
383 |
context around the matched ID for relevant metadata and positive or negative words/phrases, in
|
|
384 |
order to calculate a confidence value for each publication-->project link.
|
|
385 |
A confidence threshold is set to optimise high accuracy while minimising false positives, such
|
|
386 |
as matches with page or report numbers, post/zip codes, parts of telephone numbers, DOIs or
|
|
387 |
URLs, accession numbers.
|
|
388 |
The algorithm also applies rules for disambiguating results, as different funders can share
|
|
389 |
identical project IDs; for example, grant number 633172 could refer to H2020 project EuroMix
|
|
390 |
but
|
|
391 |
also to Australian-funded NHMRC project “Brain activity (EEG) analysis and brain imaging
|
|
392 |
techniques to measure the neurobiological effects of sleep apnea”.
|
|
393 |
Project mining works very well and was the first Text & Data Mining (TDM) service of OpenAIRE.
|
|
394 |
Performance results vary from funder to funder but precision is higher than 98% for all
|
|
395 |
funders
|
|
396 |
and 99.5% for EC projects.
|
|
397 |
Recall is higher than 95% (99% for EC projects), when projects are properly acknowledged using
|
|
398 |
project/grant IDs.
|
|
399 |
<br><br>
|
|
400 |
<span class="portal-color">Dataset extraction</span>
|
|
401 |
runs on publications full-texts as described in “High pass text-filtering for Citation
|
|
402 |
matching”, TPDL 2017[1].
|
|
403 |
In particular, we search for citations to datasets using their DOIs, titles and other metadata
|
|
404 |
(i.e., dates, creator names, publishers, etc.).
|
|
405 |
We extract parts of the text which look like citations and search for datasets using database
|
|
406 |
join and pattern matching techniques.
|
|
407 |
Based on the experiments described in the paper, precision of the dataset extraction module is
|
|
408 |
98.5% and recall is 97.4% but it is also probably overestimated since it does not take into
|
|
409 |
account corruptions that may take place during pdf to text extraction.
|
|
410 |
It is calculated on the extracted full-texts of small samples from PubMed and arXiv.
|
|
411 |
<br><br>
|
|
412 |
<span class="portal-color">Software extraction</span>
|
|
413 |
runs also on parts of the text which look like citations.
|
|
414 |
We search the citations for links to software in open software repositories, specifically
|
|
415 |
github, sourceforge, bitbucket and the google code archive.
|
|
416 |
After that, we search for links that are included in Software Heritage (SH,
|
|
417 |
https://www.softwareheritage.org) and return the permanent URL that SH provides for each
|
|
418 |
software project.
|
|
419 |
We also enrich this content with user names, titles and descriptions of the software projects
|
|
420 |
using web mining techniques.
|
|
421 |
Since software mining is based on URL matching, our precision is 100% (we return a software
|
|
422 |
link
|
|
423 |
only if we find it in the text and there is no need to disambiguate).
|
|
424 |
As for recall rate, this is not calculable for this mining task.
|
|
425 |
Although we apply all the necessary normalizations to the URLs in order to overcome usual
|
|
426 |
issues
|
|
427 |
(e.g., http or https, existence of www or not, lower/upper case), we do not calculate cases
|
|
428 |
where a software is mentioned using its name and not by a link from the supported software
|
|
429 |
repositories.
|
|
430 |
<br><br>
|
|
431 |
<span class="portal-color">For the extraction of bio-entities</span>, we focus on Protein Data
|
|
432 |
Bank (PDB) entries.
|
|
433 |
We have downloaded the database with PDB codes and we update it regularly.
|
|
434 |
We search through the whole publication’s full-text for references to PDB codes.
|
|
435 |
We apply disambiguation rules (e.g., there are PDB codes that are the same as antibody codes
|
|
436 |
or
|
|
437 |
other issues) so that we return valid results.
|
|
438 |
Current precision is 98%.
|
|
439 |
Although it's risky to mention recall rates since these are usually overestimated, we have
|
|
440 |
calculated a recall rate of 98% using small samples from pubmed publications.
|
|
441 |
Moreover, our technique is able to identify about 30% more links to proteins than the ones
|
|
442 |
that
|
|
443 |
are tagged in Pubmed xmls.
|
|
444 |
<br><br>
|
|
445 |
<span class="portal-color">Other text-mining modules</span> include mining for links to EPO
|
|
446 |
patents, or custom mining modules for linking research objects to specific research
|
|
447 |
communities,
|
|
448 |
initiatives and infrastructures, e.g. COVID-19 mining module.
|
|
449 |
Apart from text-mining modules, OpenAIRE also provides a document classification service that
|
|
450 |
employs analysis of free text stemming from the abstracts of the publications.
|
|
451 |
The purpose of applying a document classification module is to assign a scientific text one or
|
|
452 |
more predefined content classes.
|
|
453 |
In OpenAIRE, the currently used taxonomies are arXiv, MeSH (Medical Subject Headings), ACM and
|
|
454 |
DDC (Dewey Decimal Classification, or Dewey Decimal System).
|
|
455 |
<br><br>
|
|
456 |
<hr>
|
|
457 |
[1] Foufoulas, Y., Stamatogiannakis, L., Dimitropoulos, H., & Ioannidis, Y. (2017, September).
|
|
458 |
High-Pass Text Filtering for Citation Matching.
|
|
459 |
In International Conference on Theory and Practice of Digital Libraries (pp. 355-366).
|
|
460 |
Springer,
|
|
461 |
Cham.
|
498 |
462 |
</div>
|
499 |
463 |
</div>
|
500 |
|
<div *ngIf="!enrichmentMiningReadMore" class="uk-width-3-5@m uk-text-center clickable"
|
501 |
|
(click)="enrichmentMiningReadMore = true">
|
502 |
|
<a class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
|
464 |
<div *ngIf="!enrichmentMiningReadMore" class="uk-text-center clickable">
|
|
465 |
<a (click)="enrichmentMiningReadMore = true" class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
503 |
466 |
</div>
|
504 |
|
<div *ngIf="enrichmentMiningReadMore" class="uk-width-3-5@m uk-text-center clickable"
|
505 |
|
(click)="enrichmentMiningReadMore = false">
|
506 |
|
<a class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
|
|
467 |
<div *ngIf="enrichmentMiningReadMore" class="uk-text-center clickable">
|
|
468 |
<a (click)="enrichmentMiningReadMore = false" routerLink="./" fragment="tabs_card" class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
|
507 |
469 |
</div>
|
508 |
470 |
</li>
|
509 |
471 |
<li>
|
... | ... | |
521 |
483 |
<li>Zenodo community (16K results tagged)</li>
|
522 |
484 |
<li>the data source it comes from (250K results tagged)</li>
|
523 |
485 |
</ul>
|
524 |
|
The list of subjects, Zenodo communities and data sources used to enrich the products are defined
|
|
486 |
The list of subjects, Zenodo communities and data sources used to enrich the products are
|
|
487 |
defined
|
525 |
488 |
by
|
526 |
489 |
the managers of the community gateway or infrastructure monitoring dashboard associated with the
|
527 |
490 |
RC/RI.
|
... | ... | |
530 |
493 |
<li>
|
531 |
494 |
<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
|
532 |
495 |
src="assets/graph-assets/about/architecture/enrichment.svg" alt="Enrichment">
|
533 |
|
<div
|
534 |
|
[class]="'uk-margin-bottom uk-margin-medium-right uk-text-small '+(enrichmentPropagationReadMore ? '' : 'lines-18 multi-line-ellipsis')">
|
535 |
|
<div>
|
|
496 |
<div class="uk-margin-bottom uk-margin-medium-right uk-text-small lines-18"
|
|
497 |
[class.multi-line-ellipsis]="!enrichmentPropagationReadMore">
|
536 |
498 |
<div>
|
537 |
|
This process “propagates” properties and links from one product to another if between the two
|
|
499 |
This process “propagates” properties and links from one product to another if between the
|
|
500 |
two
|
538 |
501 |
there is a “strong” semantic relationship.
|
539 |
502 |
<br><br>
|
540 |
503 |
As of September 2020, the following procedures are in place:
|
... | ... | |
549 |
512 |
by”
|
550 |
513 |
a dataset D.
|
551 |
514 |
Dataset D will get the link to project P.
|
552 |
|
The relationships considered for this procedure are “isSupplementedBy” and “supplements”.
|
|
515 |
The relationships considered for this procedure are “isSupplementedBy” and
|
|
516 |
“supplements”.
|
553 |
517 |
</li>
|
554 |
518 |
<li>
|
555 |
|
Propagation of related community/infrastructure/initiative from organizations to products
|
|
519 |
Propagation of related community/infrastructure/initiative from organizations to
|
|
520 |
products
|
556 |
521 |
via affiliation relationships: e.g. a publication with an author affiliated with
|
557 |
522 |
organization O.
|
558 |
|
The manager of the community gateway C declared that the outputs of O are all relevant for
|
|
523 |
The manager of the community gateway C declared that the outputs of O are all relevant
|
|
524 |
for
|
559 |
525 |
his/her community C.
|
560 |
526 |
The publication is tagged as relevant for C.
|
561 |
527 |
</li>
|
... | ... | |
563 |
529 |
Propagation of related community/infrastructure/initiative to related products: e.g.
|
564 |
530 |
publication associated to community C is supplemented by a dataset D.
|
565 |
531 |
Dataset D will get the association to C.
|
566 |
|
The relationships considered for this procedure are “isSupplementedBy” and “supplements”.
|
|
532 |
The relationships considered for this procedure are “isSupplementedBy” and
|
|
533 |
“supplements”.
|
567 |
534 |
</li>
|
568 |
535 |
<li>
|
569 |
536 |
Propagation of ORCID identifiers to related products, if the products have the same
|
... | ... | |
573 |
540 |
the same authors as the publication. Authors of D are enriched with the ORCIDs available
|
574 |
541 |
in
|
575 |
542 |
the publication.
|
576 |
|
The relationships considered for this procedure are “isSupplementedBy” and “supplements”.
|
|
543 |
The relationships considered for this procedure are “isSupplementedBy” and
|
|
544 |
“supplements”.
|
577 |
545 |
</li>
|
578 |
546 |
</ul>
|
579 |
547 |
</div>
|
580 |
|
</div>
|
581 |
548 |
</div>
|
582 |
|
<div *ngIf="!enrichmentPropagationReadMore" class="uk-width-3-5@m uk-text-center clickable"
|
583 |
|
(click)="enrichmentPropagationReadMore = true">
|
584 |
|
<a class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
|
549 |
<div *ngIf="!enrichmentPropagationReadMore" class="uk-text-center clickable">
|
|
550 |
<a (click)="enrichmentPropagationReadMore = true" class="custom-explore-toggle">Read more<span uk-icon="chevron-down"></span></a>
|
585 |
551 |
</div>
|
586 |
|
<div *ngIf="enrichmentPropagationReadMore" class="uk-width-3-5@m uk-text-center clickable"
|
587 |
|
(click)="enrichmentPropagationReadMore = false">
|
588 |
|
<a class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
|
|
552 |
<div *ngIf="enrichmentPropagationReadMore" class="uk-text-center clickable">
|
|
553 |
<a (click)="enrichmentPropagationReadMore = false" routerLink="./" fragment="tabs_card" class="custom-explore-toggle">Read less<span uk-icon="chevron-up"></span></a>
|
589 |
554 |
</div>
|
590 |
555 |
</li>
|
591 |
556 |
</ul>
|
592 |
557 |
</div>
|
593 |
|
<!-- </div>-->
|
594 |
|
<!-- <div class="uk-width-expand">-->
|
595 |
|
<!-- <img src="assets/graph-assets/about/architecture/enrichment.svg">-->
|
596 |
|
<!-- </div>-->
|
597 |
|
</div>
|
598 |
558 |
</li>
|
599 |
559 |
<li>
|
600 |
560 |
<div class="uk-text-small uk-margin-large-top">
|
601 |
|
<!-- <div class="uk-width-3-5@m">-->
|
602 |
561 |
<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
|
603 |
562 |
src="assets/graph-assets/about/architecture/post_cleaning.svg" alt="Post Cleaning">
|
604 |
563 |
<div class="uk-margin-bottom uk-margin-medium-right">
|
605 |
564 |
<p>
|
606 |
|
The aggregation processes are continuously running and apply vocabularies as they are in a given moment of time.
|
607 |
|
It could be the case that a vocabulary changes after the aggregation of one data source has finished, thus the aggregated content does not reflect the current status of the controlled vocabularies.
|
|
565 |
The aggregation processes are continuously running and apply vocabularies as they are in a given
|
|
566 |
moment of time.
|
|
567 |
It could be the case that a vocabulary changes after the aggregation of one data source has
|
|
568 |
finished, thus the aggregated content does not reflect the current status of the controlled
|
|
569 |
vocabularies.
|
608 |
570 |
<br><br>
|
609 |
|
In addition, the integration of ScholeXplorer and DOIBoost and some enrichment processes applied on the raw and on the de-duplicated graph may introduce values that do not comply with the current status of the OpenAIRE controlled vocabularies.
|
|
571 |
In addition, the integration of ScholeXplorer and DOIBoost and some enrichment processes applied on
|
|
572 |
the raw and on the de-duplicated graph may introduce values that do not comply with the current
|
|
573 |
status of the OpenAIRE controlled vocabularies.
|
610 |
574 |
For these reasons, we included a final step of cleansing at the end of the workflow materialisation.
|
611 |
575 |
The output of the final cleansing step is the final version of the OpenAIRE Research Graph.
|
612 |
576 |
</p>
|
613 |
577 |
</div>
|
614 |
|
<!-- </div>-->
|
615 |
|
<!-- <div class="uk-width-expand">-->
|
616 |
|
<!-- <img src="assets/graph-assets/about/architecture/post_cleaning.svg">-->
|
617 |
|
<!-- </div>-->
|
618 |
578 |
</div>
|
619 |
579 |
</li>
|
620 |
580 |
<li>
|
621 |
581 |
<div class="uk-text-small uk-margin-large-top">
|
622 |
|
<!-- <div class="uk-width-3-5@m">-->
|
623 |
582 |
<img class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image"
|
624 |
583 |
src="assets/graph-assets/about/architecture/indexing.svg" alt="Indexing">
|
625 |
584 |
<div class="uk-margin-bottom uk-margin-medium-right">
|
... | ... | |
637 |
596 |
</li>
|
638 |
597 |
<li class="uk-margin-small-bottom">
|
639 |
598 |
<span class="portal-color">DSpace & EPrints</span>
|
640 |
|
repositories can install the OpenAIRE plugin to expose OpenAIRE compliant metadata records via their
|
|
599 |
repositories can install the OpenAIRE plugin to expose OpenAIRE compliant metadata records via
|
|
600 |
their
|
641 |
601 |
OAI-PMH endpoint and offer to researchers the possibility to link their depositions to the funding
|
642 |
602 |
project, by selecting it from the list of project provided by OpenAIRE
|
643 |
603 |
</li>
|
... | ... | |
647 |
607 |
Sygma automatically fetches from the OpenAIRE Search API the list of publications and datasets in
|
648 |
608 |
the
|
649 |
609 |
OpenAIRE Research Graph that are linked to the project.
|
650 |
|
The user can select the research products from the list and easily compile the continuous reporting
|
|
610 |
The user can select the research products from the list and easily compile the continuous
|
|
611 |
reporting
|
651 |
612 |
data of the project.
|
652 |
613 |
</li>
|
653 |
614 |
</ul>
|
654 |
615 |
</div>
|
655 |
|
<!-- </div>-->
|
656 |
|
<!-- <div class="uk-width-expand">-->
|
657 |
|
<!-- <img src="assets/graph-assets/about/architecture/indexing.svg">-->
|
658 |
|
<!-- </div>-->
|
659 |
616 |
</div>
|
660 |
617 |
</li>
|
661 |
618 |
<li>
|
662 |
619 |
<div class="uk-text-small uk-margin-large-top">
|
663 |
|
<!-- <div class="uk-width-3-5@m">-->
|
664 |
620 |
<img
|
665 |
621 |
class="uk-width-2-5@m uk-align-right@m uk-margin-remove-adjacent tab-image uk-padding-large uk-padding-remove-top uk-padding-remove-horizontal"
|
666 |
622 |
src="assets/graph-assets/about/architecture/stats_analysis.svg" alt="Stats Analysis">
|
... | ... | |
670 |
626 |
producing
|
671 |
627 |
the charts for funders, research initiative, infrastructures, and policy makers that you can see on
|
672 |
628 |
MONITOR.
|
673 |
|
Based on the information available on the graph, OpenAIRE provides a set of indicators for monitoring
|
|
629 |
Based on the information available on the graph, OpenAIRE provides a set of indicators for
|
|
630 |
monitoring
|
674 |
631 |
the funding and research impact and the uptake of Open Science publishing practices,
|
675 |
632 |
such as Open Access publishing of publications and datasets, availability of interlinks between
|
676 |
633 |
research
|
... | ... | |
678 |
635 |
etc.
|
679 |
636 |
</p>
|
680 |
637 |
</div>
|
681 |
|
<!-- </div>-->
|
682 |
|
<!-- <div class="uk-width-expand">-->
|
683 |
|
<!-- <img src="assets/graph-assets/about/architecture/stats_analysis.svg">-->
|
684 |
|
<!-- </div>-->
|
685 |
638 |
</div>
|
686 |
639 |
</li>
|
687 |
640 |
</ul>
|
... | ... | |
692 |
645 |
<ul class="uk-text-small portal-circle">
|
693 |
646 |
<li>
|
694 |
647 |
<a href="https://aka.ms/msracad" target="_blank">Microsoft Academic Graph</a>
|
695 |
|
which is made available under the ODC Attribution License.
|
|
648 |
which is made available under the ODC Attribution License.<br>
|
696 |
649 |
For more information on Microsoft Academic Graph please also read
|
697 |
650 |
<a href="https://docs.microsoft.com/en-us/academic-services/graph/resources-faq" target="_blank">here</a>.
|
698 |
651 |
</li>
|
... | ... | |
700 |
653 |
<a href="https://www.openaire.eu/aggregation-and-content-provision-workflows" target="_blank">https://www.openaire.eu/aggregation-and-content-provision-workflows</a>
|
701 |
654 |
</li>
|
702 |
655 |
</ul>
|
|
656 |
<a class="portal-link uk-icon-link uk-text-small uk-text-bold uk-text-uppercase" routerLink="/resources/references">
|
|
657 |
See all references <icon name="arrow_right" class="uk-margin-small-left"></icon>
|
|
658 |
</a>
|
703 |
659 |
</div>
|
704 |
660 |
</div>
|
705 |
661 |
</div>
|
706 |
662 |
<div id="metrics" class="uk-container uk-container-large uk-section">
|
707 |
663 |
<div class="uk-padding-small">
|
708 |
|
<h2 class="uk-text-center">Data & Metrics</h2>
|
709 |
|
<h4 class="uk-text-center uk-margin-medium-top portal-color">Coming soon...</h4>
|
710 |
|
<!-- <div>-->
|
711 |
|
<!-- <h3 class="uk-margin-medium-top portal-color">Data</h3>-->
|
712 |
|
<!-- <div></div>-->
|
713 |
|
<!-- </div>-->
|
714 |
|
<!-- <div>-->
|
715 |
|
<!-- <h3 class="uk-margin-medium-top portal-color">Metrics</h3>-->
|
716 |
|
<!-- <div></div>-->
|
717 |
|
<!-- </div>-->
|
|
664 |
<h2 class="uk-text-center uk-margin-xlarge-bottom">Data & Metrics</h2>
|
|
665 |
<numbers [backgroundClass]="null"></numbers>
|
718 |
666 |
</div>
|
719 |
667 |
</div>
|
720 |
668 |
<div id="infrastructure" class="uk-container uk-section">
|
... | ... | |
722 |
670 |
<h2 class="uk-text-center">Infrastructure</h2>
|
723 |
671 |
<div>
|
724 |
672 |
<div class="uk-flex uk-flex-center uk-grid uk-grid-stack">
|
725 |
|
<!-- <div>-->
|
726 |
|
<p class="uk-width-4-5@m uk-padding-small">
|
727 |
|
The OpenAIRE Research Graph is operated and maintained at the <a
|
|
673 |
<p class="uk-width-4-5@m uk-padding-small">
|
|
674 |
The OpenAIRE Research Graph is operated and maintained at the <a
|
728 |
675 |
href="https://icm.edu.pl/en/centre-of-technology/" target="_blank">ICM cutting-edge Technology centre</a>
|
729 |
|
with the facilities and staff guaranteeing robust operation of the whole system.
|
730 |
|
Okeanos SuperComputer hosting the graph consists of 26016 cores in total providing 1082 Tflops/s.
|
731 |
|
Whole setup is energy efficient with 1.554 Gflops/Watts Power Efficiency resulting in 160th place on the "Top500 by energy-eficiency" list (as of 2019).
|
732 |
|
</p>
|
733 |
|
<img class="infrastructure-image uk-margin-top uk-margin-bottom" src="assets/graph-assets/about/infrastructure.png">
|
734 |
|
<p class="uk-width-4-5@m uk-padding-small">
|
735 |
|
ICM supports the continuous operation of the infrastructure including data aggregation, deduplication, inference and provision ensuring seamless 24/7 system uptime and availability.
|
736 |
|
System administration activities cover hardware maintenance and provisioning of the new computational resources, providing High Availability solutions to address resilience to failures by service-level redundancy and Load Balancing to distribute workloads uniformly across servers.
|
737 |
|
The most crucial parts of the persisted graph are covered with backups along with well defined restore procedures.
|
738 |
|
All the monitoring activities rely on an aggregated system-level monitoring accessible via various dashboards giving the better overview of system stability and potential requirements for system elements extension.
|
739 |
|
System level monitoring is supplemented with monitoring availability of all the publicly accessible endpoints.
|
740 |
|
Hence, the offer of the public API of OpenAIRE to third parties, is of high-standards.
|
741 |
|
</p>
|
742 |
|
<p class="uk-width-4-5@m uk-padding-small">
|
743 |
|
All the maintenance operations undertaken by experienced system administrators are founded on well established routines and emergency maintenance procedures.
|
744 |
|
</p>
|
745 |
|
|
746 |
|
<!-- The OpenAIRE graph operates based on a vast variety of hardware and software. As of December 2019, the-->
|
747 |
|
<!-- hardware infrastructure is the following:-->
|
748 |
|
<!-- </p>-->
|
749 |
|
<!-- </div>-->
|
|
676 |
with the facilities and staff guaranteeing robust operation of the whole system.
|
|
677 |
Okeanos SuperComputer hosting the graph consists of 26016 cores in total providing 1082 Tflops/s.
|
|
678 |
Whole setup is energy efficient with 1.554 Gflops/Watts Power Efficiency resulting in 160th place on the
|
|
679 |
"Top500 by energy-eficiency" list (as of 2019).
|
|
680 |
</p>
|
|
681 |
<img class="infrastructure-image uk-margin-top uk-margin-bottom"
|
|
682 |
src="assets/graph-assets/about/infrastructure.png">
|
|
683 |
<p class="uk-width-4-5@m uk-padding-small">
|
|
684 |
ICM supports the continuous operation of the infrastructure including data aggregation, deduplication,
|
|
685 |
inference and provision ensuring seamless 24/7 system uptime and availability.
|
|
686 |
System administration activities cover hardware maintenance and provisioning of the new computational
|
|
687 |
resources, providing High Availability solutions to address resilience to failures by service-level
|
|
688 |
redundancy and Load Balancing to distribute workloads uniformly across servers.
|
|
689 |
The most crucial parts of the persisted graph are covered with backups along with well defined restore
|
|
690 |
procedures.
|
|
691 |
All the monitoring activities rely on an aggregated system-level monitoring accessible via various
|
|
692 |
dashboards giving the better overview of system stability and potential requirements for system elements
|
|
693 |
extension.
|
|
694 |
System level monitoring is supplemented with monitoring availability of all the publicly accessible
|
|
695 |
endpoints.
|
|
696 |
Hence, the offer of the public API of OpenAIRE to third parties, is of high-standards.
|
|
697 |
</p>
|
|
698 |
<p class="uk-width-4-5@m uk-padding-small">
|
|
699 |
All the maintenance operations undertaken by experienced system administrators are founded on well
|
|
700 |
established routines and emergency maintenance procedures.
|
|
701 |
</p>
|
750 |
702 |
</div>
|
751 |
703 |
</div>
|
752 |
704 |
</div>
|
... | ... | |
756 |
708 |
<h2 class="uk-text-center">Team</h2>
|
757 |
709 |
<div>
|
758 |
710 |
<div class="uk-margin-bottom">
|
759 |
|
<!-- <div class="uk-flex uk-flex-middle uk-grid" uk-grid="">-->
|
760 |
|
<!-- <div class="uk-text-center uk-width-1-1@s uk-width-1-3@m uk-first-column">-->
|
761 |
|
<!-- <img src="assets/graph-assets/about/team.svg">-->
|
762 |
|
<!-- </div>-->
|
763 |
|
|
764 |
711 |
<img class="uk-align-center uk-align-left@m uk-margin-remove-adjacent"
|
765 |
712 |
src="assets/graph-assets/about/team.svg" alt="Team">
|
766 |
713 |
|
... | ... | |
768 |
715 |
<div class="uk-margin-medium-bottom">
|
769 |
716 |
Key team members contributing to the Research Graph
|
770 |
717 |
</div>
|
771 |
|
<div>
|
772 |
|
<a class="uk-button portal-button" target="_blank" href="https://www.openaire.eu/research-graph-team">
|
|
718 |
<div><a class="uk-button portal-button" routerLink="./team">
|
773 |
719 |
Meet the team
|
774 |
720 |
<icon name="arrow_right" ratio="0.8" class="space"></icon>
|
775 |
721 |
</a>
|
776 |
722 |
</div>
|
777 |
723 |
</div>
|
778 |
|
<!-- </div>-->
|
779 |
724 |
</div>
|
780 |
725 |
</div>
|
781 |
726 |
</div>
|
[Graph | Trunk]: Create Team and References pages. Change about architecture images