{"id":11054,"date":"2022-12-09T10:52:48","date_gmt":"2022-12-09T10:52:48","guid":{"rendered":"https:\/\/www.science.orphadata.comorphapackets\/"},"modified":"2025-12-10T14:22:56","modified_gmt":"2025-12-10T14:22:56","slug":"orphapackets","status":"publish","type":"page","link":"https:\/\/sciences.orphadata.com\/orphapackets\/","title":{"rendered":"ORPHApackets"},"content":{"rendered":"
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ORPHApackets releases are produced twice a year (in June and December), synchronized with the generation of ORDO, and are freely available in a dedicated\n GitHub <\/a>repository.\u200b\u200b<\/p>\n

An ORPHApacket is a formalised data sharing container embedding \u201cpieces\u201d of knowledge related to known rare disorders derived from the Orphanet knowledge database and ORDO (Orphanet Rare Diseases Ontology). The ORPHApacket format is\n encoded in JSON or YAML.\u200b<\/p>\n

Orphapackets are available for download, below via the\n CC BY 4.0 licence<\/a>.<\/p>\n <\/div>\n <\/div>\n

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Orphapackets release of December 2025<\/strong><\/p>\n <\/div>\n <\/div>\n

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\n \n \n Access to ORPHApackets releases<\/span>\n
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\n ORPHApackets releases <\/a>\n <\/p>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n

\n \n \n More on ORPHApackets<\/span>\n
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An ORPHApacket <\/strong>is a formalized data sharing container embedding ”<\/span>pieces\n ” <\/span>of knowledge related to known rare disorders derived from the Orphanet knowledge database and ORDO (Orphanet Rare Diseases Ontology). The ORPHApacket format is encoded in JSON or YAML.<\/p>\n

An ORPHApacket includes among other (see figure at the bottom):<\/p>\n

     \u2022 <\/span>ORPHApacket ID (an ORPHAcode for an already known concept in the Orphanet database or\n a specific ID with ”RD_” prefix if it is a not yet known concept in ORDO)<\/p>\n

     <\/span>\u2022 Label with the language of the label (English by default)<\/p>\n

     <\/span>\u2022 An ORPHAcode (if an already known concept), and its PURL (Persistent URL) to the concept in\n ORDO<\/p>\n

     <\/span>\u2022 Version and the date of Orphanet Database extraction used to produce the ORPHApacket.<\/p>\n

     <\/span>\u2022 Type which differs depending on the level of granularity of each clinical concept defined as\n follows (see Figure 1 below):<\/p>\n

          <\/span>o Group of disorder<\/strong> is\n defined as a \u201cclinical entity defined by a set of phenotypic abnormalities shared by several diseases, malformation or clinical syndromes, morphological or biological anomalies, and particular clinical situations in a disease\n or a syndrome and used to group them together.\u201d<\/p>\n

          <\/span>o Disorder <\/strong>is\n a ”<\/span>clinical entity defined by the comprehensive set of phenotypic abnormalities characterizing it. It can be a disease,\n a malformation or clinical syndrome, a morphological or biological anomaly or a particular clinical situation in a disease or a syndrome”<\/span>.<\/p>\n

          <\/span>o Subtype of disorder<\/strong> is\n a ”<\/span>subdivision <\/span>of\n a disease, malformation syndrome, morphological anomaly, biological anomaly, clinical syndrome or particular clinical situation in a disease or a syndrome further defined by its particular clinical presentation.”<\/span> It\n can be a clinical subtype, an etiological subtype or a histopathological subtype.<\/p>\n <\/div>\n <\/div>\n

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Depending on the available data, especially the level of granularity of each concept, an ORPHApacket <\/strong>can also contain:<\/p>\n

     <\/span>\u2022 Concept definition<\/p>\n

     <\/span>\u2022 List of synonyms<\/p>\n

     <\/span>\u2022 Average age of onset of the disorder<\/p>\n

     <\/span>\u2022 Mode of inheritance<\/p>\n

     <\/span>\u2022 Epidemiological annotations<\/p>\n

     <\/span>\u2022 ”Subclass of” list with reference to ”upper” concepts in ORDO, with label of those upper\n concepts, ORPHA number and PURL.<\/p>\n

     <\/span>\u2022 ”HasSubtype” <\/span>list\n with reference to ”<\/span>child” <\/span>concept\n in ORDO, with label of those concepts, ORPHAnumber, PURL,<\/p>\n

     <\/span>\u2022 Gene-Disorder association including the HGNC gene label and symbol, external reference to OMIM\n and HGNC<\/p>\n

     <\/span>\u2022 HPO-disorder association together with its related list of HPO Id, HPO English label with their\n frequency of occurrence for the specific disease concept (including negative relationship (i.e. HPO term always absent for a given disease), PURL of the HPO concept.<\/p>\n

Here is schematized the contain of an ORPHApacket:<\/p>\n <\/div>\n <\/div>\n

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As explained before, depending of the type of concept (group of disorder, disorder or subtype of disorder), an ORPHApacket <\/span>will contain more or less information. Less in the case of an\n ORPHApacket <\/span>dedicated to a \u201cgroup of disorder\u201d concept, more for an ORPHApacket <\/span>related to a \u201cdisorder\u201d concept or a \u201csubtype\u201d concept, for instance\n including gene data. ORPHApackets <\/span>could be enriched afterwards with any relevant piece of information, therefore making its content evolving in time to fit the needs of the project.<\/p>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n

\n \n \n References and Contact<\/span>\n
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