The databases downloadable here (from version 3.0 on) have been created using the new database schema (The schema and database information is available here).
Note that the database file named "WHOLEDB" contains the entire database except the ENTITY table, which the new database provides. The individual tables are also provided separately. Users can download the entire database at once or the individual tables separately depending on their needs. The file names consist of four parts: database name _ R (or A) _ table name _ PubMed to date. The letter R represents that the database was generated with standard SemRep options, whereas A denotes that it was generated with the anaphora resolution option.
The new database schema differs from the previous one (versions 2X) in the following ways:
For semmedVER31_R, we have generated anew the entire database, to resolve an issue reported in the previous version in which some predications were found to have the wrong combination of subject name and subject semantic type or object name and object semantic type. semmedVER31_R has also been enhanced with two new columns, SECTION_HEADER and NORMALIZED_SECTION_HEADER, in the SENTENCE table. These columns are used to store the section information of structured abstracts if the original citations provide that information.
The GENERIC_CONCEPT table has been updated in the June 30 2018 and all subsequent releases. Consequently, the SUBJECT_NOVELTY and OBJECT_NOVELTY columns of the PREDICATION table have been updated as follows: If the concept is not in the GENERIC_CONCEPT table, the value is set to 1; otherwise, it is set to 0.
Starting with version VER40, the PMID column in SENTENCE is dependent on the PMID in the CITATION table with a foreign key constraint. Therefore, all the PMIDs in the SENTENCE table have corresponding rows in the CITATION table, which has metadata PMID information.
| TABLE NAME | Size | # Rows | Download link | sha1sum | md5sum |
|---|---|---|---|---|---|
| Entire Database | 18G | N/A | download | download | download |
| CITATIONS | 142M | 30,439,312 | download | download | download |
| ENTITY | 33G | 1,369,836,547 | download | download | download |
| GENERIC_CONCEPT | 4.7K | 259 | download | download | download |
| PREDICATION | 2.5G | 103,284,300 | download | download | download |
| PREDICATION_AUX | 3.1G | 103,208,390 | download | download | download |
| SENTENCE | 12G | 199,843,876 | download | download | download |
| TABLE NAME | Size | # Rows | Download link | sha1sum | md5sum |
|---|---|---|---|---|---|
| Entire Database | 18G | N/A | download | download | download |
| CITATIONS | 141M | 30,426,087 | download | download | download |
| ENTITY | 33G | 1,369,836,668 | download | download | download |
| GENERIC_CONCEPT | 4.7K | 259 | download | download | download |
| PREDICATION | 2.5G | 103,156,767 | download | download | download |
| PREDICATION_AUX | 3.1G | 103,156,767 | download | download | download |
| SENTENCE | 12G | 199,751,911 | download | download | download |
| TABLE NAME | Size | Download link | sha1sum | md5sum |
|---|---|---|---|---|
| Entire Database | 17.6G | download | download | download |
| CITATIONS | 140M | download | download | download |
| ENTITY | 33G | download | download | download |
| GENERIC_CONCEPT | 4.5K | download | download | download |
| METAINFO | 802 | download | download | download |
| PREDICATION | 2.51G | download | download | download |
| PREDICATION_AUX | 3.15G | download | download | download |
| SENTENCE | 11.8G | download | download | download |
| TABLE NAME | START DATE | END DATE | Size | Download link | sha1sum | md5sum |
|---|---|---|---|---|---|---|
| Entire Database | 1865 | June 30 2018 | 17.7G | download | download | download |
| CITATIONS | 1865 | June 30 2018 | 140M | download | download | download |
| ENTITY | 1865 | June 30 2018 | 36G | download | download | download |
| GENERIC_CONCEPT | N/A | N/A | 4.5K | download | download | download |
| METAINFO | N/A | N/A | 802 | download | download | download |
| PREDICATION | 1865 | June 30 2018 | 2.47G | download | download | download |
| PREDICATION_AUX | 1865 | June 30 2018 | 3.12G | download | download | download |
| SENTENCE | 1865 | June 30 2018 | 11.9G | download | download | download |
| TABLE NAME | START DATE | END DATE | Size | Download link | sha1sum | md5sum |
|---|---|---|---|---|---|---|
| Entire Database | 1865 | Dec 31 2017 | 17.1G | download | download | download |
| CITATIONS | 1865 | Dec 31 2017 | 136M | download | download | download |
| ENTITY | 1865 | Dec 31 2017 | 33G | download | download | download |
| GENERIC_CONCEPT | N/A | N/A | 129K | download | download | download |
| METAINFO | N/A | N/A | 778 | download | download | download |
| PREDICATION | 1865 | Dec 31 2017 | 2.41G | download | download | download |
| PREDICATION_AUX | 1865 | Dec 31 2016 | 3.05G | download | download | download |
| SENTENCE | 1865 | Dec 31 2017 | 11.5G | download | download | download |
| TABLE NAME | START DATE | END DATE | Size | Download link | sha1sum | md5sum |
|---|---|---|---|---|---|---|
| Entire Database | 1865 | June 30 2017 | 16.3G | download | download | download |
| CITATIONS | 1865 | June 30 2017 | 129M | download | download | download |
| ENTITY | 1865 | June 30 2017 | 32G | download | download | download |
| GENERIC_CONCEPT | N/A | N/A | 129M | download | download | download |
| METAINFO | N/A | N/A | 764 | download | download | download |
| PREDICATION | 1865 | June 30 2017 | 2.34G | download | download | download |
| PREDICATION_AUX | 1865 | June 30 2016 | 2.96G | download | download | download |
| SENTENCE | 1865 | June 30 2017 | 10.8G | download | download | download |
| TABLE NAME | START DATE | END DATE | Size | Download link | sha1sum | md5sum |
|---|---|---|---|---|---|---|
| Entire Database | 1865 | Dec 31 2016 | 16.2G | download | download | download |
| CITATIONS | 1865 | Dec 31 2016 | 129M | download | download | download |
| COREFERENCE | 1865 | Dec 31 2016 | 450M | download | download | download |
| ENTITY | 1865 | Dec 31 2016 | 29G | download | download | download |
| GENERIC_CONCEPT | 1865 | Dec 31 2016 | 129M | download | download | download |
| METAINFO | N/A | N/A | 764 | download | download | download |
| PREDICATION | 1865 | Dec 31 2016 | 2.29G | download | download | download |
| PREDICATION_AUX | 1865 | Dec 31 2016 | 2.87G | download | download | download |
| SENTENCE | 1865 | Dec 31 2016 | 10.5G | download | download | download |
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