# DOIBoost: Crossref, Unpaywall, Microsoft Academic Graph, ORCID

DOIBoost is a dataset that combines research outputs and links among them from a selection of data sources. 
It enriches the records available on Crossref with what's available on Unpaywall, Microsoft Academic Graph, ORCID intersecting all those datasets by DOI. 
As consequence, DOIBoost does not contain any record from MAG, Unpaywall, or ORCID that doesn't provide a DOI available in Crossref.

Each Crossref record is enriched with:
* ORCID identifiers of authors from ORCID
* Open Access instance (with OA color/route and license) from Unpaywall
* the following information from MAG:
    * abstracts
    * MAG identifiers of authors
    * affiliation (result - organization) relationships
    * subjects (MAG FieldsOfStudy)
    * conference or journal information

The Open Access status is also set by intersecting the journal information of a record with the journal lists available from DOAJ and the Gold ISSN list.

## Inputs

* *Crossref*: dump available to Crossref subscribers via MetadataPlus service, updated once a month.
* *Microsoft Academic Graph*: downloaded version on 2021-02-15. We plan to take the latest version in Dec 2021 before MAG will be retired.
* *ORCID*: baseline dump obtained in 2020-10-13, regularly updated every week from the [ORCID public API](https://info.orcid.org/documentation/features/public-api).
* *Unpaywall*: public database snapshot downloaded in March 2021. Unpaywall updates it twice a year (https://unpaywall.org/products/snapshot)

The construction of the DOIBoost dataset consists of the following phases:

## Process

The following section describes the processing steps needed to build DOIBoost starting from the input data.

### Crossref filtering

Records in Crossref are ruled out according to the following criteria

* have blank title, examples:
    * `10.1093/rheumatology/41.7.837`
    * `10.1093/qjmed/95.7.430`
    * `10.1371/journal.pone.0171434.g005`
* have one of the following publishers: `"Test accounts"`, `"CrossRef Test Account"`
    * Examples from https://api.crossref.org/works?query.publisher-name=%22Test%20accounts%22
        * `10.1007/bf00344543`
        * `10.1007/bf00186154`
        * `10.1306/64ed947a-1724-11d7-8645000102c1865d`
* have no authors with valid names, where valid means: not blank and different from all strings in this list: `List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;")`
    * Examples for blank authors:
        * `10.1108/00070709810247807`
        * `10.1016/s1074-9098(02)00346-5`
        * `10.1136/heart.88.1.6`
    * Examples for `"none"` author from https://api.crossref.org/works?query.author=%22none%22
        * `10.4007/annals.2016.184.3.11`
        * `10.4007/annals.2012.176.1.6`
        * `10.2172/6393585`
    * Examples for `"test"` author from https://api.crossref.org/works?query.author=%22test%22
        * `10.5116/ijme.54ca.a5ae`
        * `10.5755/j01.ss.71.2.544`
        * `10.5755/j01.ee.22.2.319`
* have `"Addie Jackson"` as author and `"Elsevier BV"` as publisher (empirically we say they are test records)
    * Examples from https://api.crossref.org/works?query.author=Addie+Jackson&query.publisher-name=%22Elsevier%20BV%22
        * `10.2139/ssrn.2082156`
        * `10.2139/ssrn.2202300`
        * `10.2139/ssrn.2255657`
* have not one of the following values in the field `type` : `"book-section"`, `"book"`, `"book-chapter"`, `"book-part"`, `"book-series"`, `"book-set"`, `"book-track"`, `"edited-book"`, `"reference-book"`, `"monograph"`, `"journal-article"`, `"dissertation"`, `"other"`, `"peer-review"`, `"proceedings"`, `"proceedings-article"`, `"reference-entry"`, `"report"`, `"report-series"`, `"standard"`, `"standard-series"`, `"posted-content"`, `"dataset"`,
    * Example:
        * `10.1371/journal.pone.0171434.g005`
        * `10.7554/elife.21052.049`
        * `10.1371/journal.pcbi.1005379.s006`

Records with `type=dataset` are mapped into OpenAIRE results of type dataset. All others are mapped as OpenAIRE results of type publication.

### Mapping Crossref properties into the OpenAIRE Research Graph

Properties in OpenAIRE results are set based on the logic described in the following table:

| OpenAIRE Result field path             | Crossref path(s)                                                   | Notes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
|----------------------------------------|--------------------------------------------------------------------| |
| `id`                                   | `doi`                                                              | id in the form `doi_________::md5(doi)`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| `dateofcollection`                     | `indexed.datetime`                                                 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `lastupdatetimestamp`                  | `indexed.timestamp`                                                |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `type`                                 | `type`                                                             | `dataset` if the Crossref type is dataset, `publication` otherwise (based on the filtering logics described above)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| `originalId`                           | `doi, clinical-trial-number, alternative-id`                       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `pid`                                  |                                                                    | The scheme tells the type of PID, the value contains the actual value                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| `pid.scheme`                           |                                                                    | Default value: doi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| `pid.value`                            | `doi`                                                              | The doi is normalised and lower-cased                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| `maintitle`                            | `title`                                                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `subtitle`                             | `subtitle`                                                         |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `author`                               | `author`                                                           | if available the sequence is mapped to rank and the ORCID is also mapped                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| `author.name`                          | `author.given`                                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `author.surname`                       | `author.family`                                                    |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `author.fullname`                      | `author.given author.family`                                       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `author.rank`                          |                                                                    | based on the order, starts from 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| `author.pid`                           |                                                                    | only if the ORCID is available                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
| `author.pid.id.scheme`                 |                                                                    | Default `'pending_orcid'` (meaning that it is not an id confirmed by ORCID)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| `author.pid.id.value`                  | `author.ORCID`                                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `author.pid.provenance.provenance`     |                                                                    | Default 'Harvested'                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
| `author.pid.provenance.trust`          |                                                                    | Default '0.9'                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
| `description`                          | `abstract`                                                         |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `subject`                              | `subject`                                                          | with `classid='keywords'`, i.e. no controlled vocabularies for Crossref subjects                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
| `publicationdate`                      | `issued.datetime` or, if not available, `created.datetime`         |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `publisher`                            | `publisher`                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `source`                               | `source`                                                           | only if the record is not of type `book`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| `source`                               | concatenation of `container-title.head` + `"ISBN: "` + `ISBN.head` | only if the record is of type `book`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| `container`                            |                                                                    | It is set only for publications with information about the journal it was published in.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| `container.name`                       | `container-title.head`                                             |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `container.issnOnline`                 | `issn-type.value`                                                  | if `issn-type.type='electronic'`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
| `container.issnPrinted`                | `issn-type.value`                                                  | if `issn-type.type='print'`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| `container.vol`                        | `volume`                                                           |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `container.sp`                         | `page`                                                             | before `'-'`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| `container.ep`                         | `page`                                                             | after `'-'`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| `instance`                             |                                                                    | One instance is created with the DOI URL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| `instance.accessright`                 |                                                                    | Values in `instance.accessright.code` and `instance.accessright.label` are set based on license and dateofacceptance:<br/>- `UNKNOWN`: if the license is blank<br/>- `OPEN ACCESS`: if the license is a CC license or an ACS license or an APA license (considered OPEN also by Unpaywall, see [Unpaywall FAQ](https://support.unpaywall.org/support/solutions/articles/44002063718-what-is-an-oa-license-) for details) or if OUP license, but only after 12 months from the publication date<br/>- `EMBARGO`: OUP license, before 12 months from the publication date<br/>- `CLOSED`: if there is a license not covered by the previous cases |
| `instance.accessright.code`            |                                                                    | Code from the [COAR vocabulary for access right](http://vocabularies.coar-repositories.org/documentation/access_rights/)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| `instance.accessright.label`           |                                                                    | One of: `OPEN`, `RESTRICTED`, `CLOSED`, `EMBARGO`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| `instance.accessright.scheme`          |                                                                    | Scheme that defines the code and label, i.e. the URL to the [COAR vocabulary for access right](http://vocabularies.coar-repositories.org/documentation/access_rights/)                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
| `instance.accessright.openAccessRoute` |                                                                    | only if `instance.accessright.value = 'OPEN ACCESS'`. Default is `hybrid`. The route is fixed in subsequent phases of DOIBoost, namely when intersecting with Unpaywall and patching the hostedby via DOAJ and the Gold-ISSN list.                                                                                                                                                                                                                                                                                                                                                                                                              |
| `instance.license`                     | `license.URL `                                                     | If there is a `license.content-version='vor'`, then this is used. Otherwise the first license entry is used.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| `instance.pid`                         |                                                                    | The scheme tells the type of PID, the value contains the actual value                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| `instance.pid.scheme`                  |                                                                    | Default value: `doi`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| `instance.pid.value`                   | `doi`                                                              | The doi is normalised and lower-cased                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| `instance.publicationdate`             | `issued.datetime` or, if not available, `created.datetime`         |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| `instance.refereed`                    |                                                                    | set to `peerReviewed` only if `relation.has-review.id` is not empty, `UNKNOWN` otherwise.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| `instance.type`                        | `subtype`                                                          | mapped using the [OpenAIRE vocabulary for result typologies](https://api.openaire.eu/vocabularies/dnet:result_typologies)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| `instance.url`                         | `doi`                                                              | Full URL of the DOI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |

All other fields of the Json schema not mentioned in the table contain empty values.

All the records from Crossref are related to the datasource with `name=Crossref` and `id=openaire____::081b82f96300b6a6e3d282bad31cb6e2`

Possible improvements:
* map `clinical-trial-number` and `alternative-id` in `alternateIdentifiers`?
* Verify if Crossref has a property for `language`, `country`, `container.issnLinking`, `container.iss`, `container.edition`, `container.conferenceplace` and `container.conferencedate`
* Different approach to set the `refereed` field and improve its coverage?

h3. 2 Map Crossref links to projects/funders

Links to funding available in Crossref are mapped as funding relationships (`result -- isProducedBy -- project`) applying the following mapping:

| Funder                                                                                                                                                                                       | Grant code                                                                               | Link to                                                                                                                                             |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|
| DOI: `{10.13039/100010663, 10.13039/100010661, 10.13039/501100007601, 10.13039/501100000780, 10.13039/100010665}` or name: `'European Union’s Horizon 2020 research and innovation program'` | series of `4-9` digits in `award`                                                        | Link to H2020 project                                                                                                                               |
| DOI: `{10.13039/100011199, 10.13039/100004431, 10.13039/501100004963, 10.13039/501100000780}`                                                                                                | series of `4-9` digits in `award`                                                        | Link to FP7 project                                                                                                                                 |
| DOI: `10.13039/501100000781` OR name: `'European Union's'`                                                                                                                                   | series of `4-9` digits in `award`                                                        | Link to FP7 or H2020 project                                                                                                                        |
| DOI: `10.13039/100000001`                                                                                                                                                                    | `award`                                                                                  | Link to NSF project                                                                                                                                 |
| DOI: `10.13039/501100001665` OR name: `{'The French National Research Agency (ANR)', 'The French National Research Agency'}`                                                                 | `award`                                                                                  | Link to ANR project                                                                                                                                 |
| DOI: `10.13039/501100002341`                                                                                                                                                                 | `award`                                                                                  | Link to Academy of Finland project                                                                                                                  |
| DOI: `10.13039/501100001602`                                                                                                                                                                 | `award`, removing the initial 'SFI' if present                                           | Link to SFI project                                                                                                                                 |
| DOI: `10.13039/501100000923`                                                                                                                                                                 | `award`                                                                                  | Link to ARC project                                                                                                                                 |
| DOI: `10.13039/501100000038`                                                                                                                                                                 | `award` ignore: we cannot map the project codes in Crossref to project codes in OpenAIRE | Link to NSERC (`unidentified` project)                                                                                                              |
| DOI: `10.13039/501100000155`                                                                                                                                                                 | `award` ignore: we cannot map the project codes in Crossref to project codes in OpenAIRE | Link to SSHRC (`unidentified` project)                                                                                                              |
| DOI: `10.13039/501100000024`                                                                                                                                                                 | `award` ignore: we cannot map the project codes in Crossref to project codes in OpenAIRE | Link to CIHR (`unidentified` project)                                                                                                               |
| DOI: `10.13039/501100002848` OR name :`'CONICYT, Programa de Formación de Capital Humano Avanzado'`                                                                                          | `award`                                                                                  | Link to CONICYT project                                                                                                                             |
| DOI: `10.13039/501100003448`                                                                                                                                                                 | series of `4-9` digits in award                                                          | Link to GSRT project                                                                                                                                |
| DOI: `10.13039/501100010198`                                                                                                                                                                 | `award`                                                                                  | Link to SGOV project                                                                                                                                |
| DOI: `10.13039/501100004564`                                                                                                                                                                 | series of `4-9` digits in award                                                          | Link to MESTD project                                                                                                                               |
| DOI: `10.13039/501100003407`                                                                                                                                                                 | `award`                                                                                  | Link to MIUR project. Since OpenAIRE has a small subset of MIUR projects, a link to the MIUR funder (`unidentified`<br/> project) is also generated |
| DOI: `{10.13039/501100006588, 10.13039/501100004488}`                                                                                                                                        | `award`, removing `'Project No'` and `'HRZZ'` prefix, if present                         | Link to HRZZ or MZOS project                                                                                                                        |
| DOI: `10.13039/501100006769`                                                                                                                                                                 | `award`                                                                                  | Link to Russian Science Foundation project                                                                                                          |
| DOI: `10.13039/501100001711`                                                                                                                                                                 | `award` after `'_'` and before `'/'`                                                     | Link to SNSF project                                                                                                                                |
| DOI: `10.13039/501100004410`                                                                                                                                                                 | `award`                                                                                  | Link to TUBITAK project                                                                                                                             |
| DOI: `10.10.13039/100004440`  or name: `Wellcome Trust Masters Fellowship`                                                                                                                   | `award`                                                                                  | Link to Wellcome Trust specific project and to the `unidentified` project.                                                                          |

### Intersect Crossref with UnpayWall by DOI

The fields we consider from UnpayWall are:
* `is_oa`
* `best_oa_location`
* `oa_status`

The results of Crossref that intersect by DOI with UnpayWall records are enriched with one additional `instance` with the following properties:

| OpenAIRE Result field path             | Unpaywall field path       | Notes                                                                                                                                                                  |
|----------------------------------------|----------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `instance`                             |                            | created only if `is_oa` and a `best_oa_location` is available                                                                                                          |
| `instance.accessright`                 |                            | default value `Open Access`: we do not add instances if UnpayWall says there is no open version                                                                        |
| `instance.accessright.code`            |                            | Open Access code from the [COAR vocabulary for access right](http://vocabularies.coar-repositories.org/documentation/access_rights/)                                   |
| `instance.accessright.label`           |                            | Always `OPEN`                                                                                                                                                          |
| `instance.accessright.scheme`          |                            | Scheme that defines the code and label, i.e. the URL to the [COAR vocabulary for access right](http://vocabularies.coar-repositories.org/documentation/access_rights/) |
| `instance.accessright.openAccessRoute` | `oa_status`                |                                                                                                                                                                        |
| `instance.url`                         | `best_oa_location`         |                                                                                                                                                                        |
| `instance.license`                     | `best_oa_location.license` |                                                                                                                                                                        |
| `instance.pid`                         |                            | The scheme tells the type of PID, the value contains the actual value                                                                                                  |
| `instance.pid.scheme`                  |                            | Default value: `doi`                                                                                                                                                   |
| `instance.pid.value`                   | `doi`                      | The doi is normalised and lower-cased                                                                                                                                  |

For the definition of UnpayWall's `oa_status` refer to the [Unpaywall FAQ](https://support.unpaywall.org/support/solutions/articles/44001777288-what-do-the-types-of-oa-status-green-gold-hybrid-and-bronze-mean-)

The record will also feature a relation to the UnpayWall data source: `name="UnpayWall"`, `id=openaire____::8ac8380272269217cb09a928c8caa993`.

### Intersect with ORCID

The fields we consider from ORCID are:
* `doi`
* `authors`, a list of authors, each with optional `name`, `surname`, `creditName`, `oid`

| OpenAIRE field path                | ORCID path            | Notes                                                                                                                                |
|------------------------------------|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------|
| `pid`                              | `doi`                 |                                                                                                                                      |
| `author.name`                      | `capitalize(name)`    | only mapped if not blank                                                                                                             |
| `author.surname`                   | `capitalize(surname)` | only mapped if not blank                                                                                                             |
| `author.fullname`                  |                       | if name and surname are not blank, they are concatenated (`capitalize(name) capitalize(surname)`), otherwise we use the `creditName` |
| `author.pid`                       |                       | only if the `ORCID` is available                                                                                                     |
| `author.pid.id.scheme`             |                       | Default `orcid` (meaning that it is confirmed by ORCID, (in contrast to the `orcid_pending` set from Crossref and Unpaywall)         |
| `author.pid.id.value`              | `oid`                 |                                                                                                                                      |
| `author.pid.provenance.provenance` |                       | Default `Harvested`                                                                                                                  |
| `author.pid.provenance.trust`      |                       | Default `0.9`                                                                                                                        |

The records are enriched with the ORCID identifiers of their authors.

[//]: # (TODO: Update with the new approach implemented by Miriam.)

The current approach is:
* if the number of authors from Crossref equals the size of authors from ORCID, then we pick the list of authors with more PIDs and try to enrich it with the PIDs from the other list, based on JaroWrinkler distance on authors' names, surnames, or fullnames, depending on which properties are available;
* if the number of authors are different, then we take the longest and try to enrich it with the PIDs from the other author list, based on JaroWrinkler distance on authors' names, surnames, or fullnames, depending on which properties are available

Miriam will modify the process to ensure that:
* the list of authors from Crossred always "win"
* the identifiers from ORCID "win"

### Intersect with Microsoft Academic Graph

*Important Notes*
* Only papers with DOI are considered
* Since for the same DOI we have multiple version of item with different MAG PaperId, we only take one per DOI (the last one we process). We call this dataset `Papers_distinct`

When mapping MAG records to the OpenAIRE Research Graph, we consider the following MAG tables:
* `PaperAbstractsInvertedIndex`: for the paper abstracts
* `Authors`: for the authors. The MAG data is pre-processed by grouping authors by PaperId
* `Affiliations` and `PaperAuthorAffiliations`: to generate links between publications and organisations
* `Journals` and `ConferenceInstances`: joined with `Papers_distinct` to have the information about the venues where the paper was published
* TO BE REMOVED `PaperUrls`: to create one instance for the OpenAIRE publication
* `FieldsOfStudy`: to add subjects

The records are enriched with:
* abstracts
* MAG identifiers of authors
* affiliation relationships
* subjects (MAG FieldsOfStudy)
* conference or journal information (in the `journal` field) TODO: or `container`, in case of the dump?
* [TO BE REMOVED] instances with URL from MAG

### Enrich DOIBoost3 with hosting data sources (`hostedby`) and access right information

In this phase, we intersect DOIBoost3 with a dataset composed of journals from OpenAIRE, Crossref, and the ISSN gold list. Each journal comes with its International Standard Serial Numbers (`issn`, `eissn`, `lissn`) and, when available, a flag that tells if the journal is open access. The intersection is done on the basis of the International Standard Serial Numbers. The records with a `journal.[l|e]issn` that match are enriched as follows:
* Each instance gain the `hostedby` information corresponding to the journal
* If the journal is open access, the access rights of the instances are also set to `Open Access` with `gold` route (because by construction, the journals we know are open are from DOAJ or Gold ISSN list)

The hostedby of records that do not match are set to the `Unknown Repository`.

## References

The idea behind DOIBoost and its origin can be found in the paper (and related resources) at:

* La Bruzzo S., Manghi P., Mannocci A. (2019) OpenAIRE's DOIBoost - Boosting CrossRef for Research. In: Manghi P., Candela L., Silvello G. (eds) Digital Libraries: Supporting Open Science. IRCDL 2019. Communications in Computer and Information Science, vol 988. Springer, doi:10.1007/978-3-030-11226-4_11 . Open Access version available at: [10.5281/zenodo.1441071](https://doi.org/10.5281/zenodo.1441071)
