Published March 25, 2022
| Version v15
Dataset
Open
PMDB: a relational database for PubMed
Description
The files constitute a compressed dump of PMDB, which was created in PostgreSQL 14 using the pmparser R package. Apologies for having to download the files individually, Zenodo's API has become unable to accept one 25 GB file. Once you have a Postgres server running, you can set up the database as follows:
1. Move the downloaded files to a new folder.
2. Restore the database onto your Postgres server. Below is one way. Replace <...> as appropriate, substituting <dump_name> with the name of the new folder containing the dump files. This will take some time, so use as many cores as you can spare. Beware the full database is about 136 GB.
createdb -h <host_name> -U <user_name> pmdb
pg_restore -j <num_cores> --no-privileges --no-owner -h <host_name> -U <user_name> -d pmdb <dump_name>MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLM's Terms and Conditions.
Files
Files
(25.3 GB)
| Name | Size | Download all |
|---|---|---|
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md5:7d84e8407f93d0d6fd96165dacaa685f
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1.9 kB | Download |
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md5:ed0f1f67c92c4bc58353d50325ccbb51
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245.1 MB | Download |
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md5:0833c94534c965881e50be4d428ea40d
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1.4 GB | Download |
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md5:526cda87ee057124156217b851575387
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347.9 MB | Download |
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md5:a7f81cd1c596401cdddd76106ad618bf
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191.3 MB | Download |
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md5:fa62cc122bbca90c87560db62bd23846
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423.7 MB | Download |
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md5:e4bc0017690c8d00f9b7128e3d120587
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11.4 MB | Download |
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md5:db3b12b16023346a392d2656d213a659
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2.9 GB | Download |
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md5:d4deb5ae1dd31898ef81bd531ee61283
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679.4 MB | Download |
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md5:d4b905fab59b8cc05ed8a8433a84cda5
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22.4 MB | Download |
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md5:de5691835e95d0503067358f505c60b6
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340.6 MB | Download |
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md5:d02dbf3653da5e2af248b82198bc288e
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10.0 MB | Download |
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md5:5bbfbb0c6c365c56e849c80e29203c67
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105.7 MB | Download |
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md5:e15d916b71fc6a4f9b4edf3569f17654
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670.6 MB | Download |
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md5:884e2344c5272cc6cd8bd95b8471d60a
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14.0 MB | Download |
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md5:1cb452a102820c95724a036cb003f52f
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16.6 MB | Download |
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md5:f61d5bd82cbc8b2698cc11d6fbc87ecb
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46.2 MB | Download |
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md5:731a23c7ee9402875281e0843fccaf51
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10.6 GB | Download |
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md5:0d50a8156154a51038c804b9df917983
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1.7 GB | Download |
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md5:c803d2a2cd75a432915a7355250a68f4
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1.7 GB | Download |
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md5:049532de61ad43664b930305662c42ce
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52.6 MB | Download |
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md5:c2c81872347bc45259718b4542178da3
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7.1 MB | Download |
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md5:00d5c1102010f1a55fe2bee924fc640c
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77.0 MB | Download |
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md5:c7476b421d350c2d519ce1abe750f968
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46.2 MB | Download |
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md5:c0879c0ad164f4c4e6eaac1158e4ff4f
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1.4 MB | Download |
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md5:97d3ce39124a22a23e04f79b3e0bf60c
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3.1 kB | Download |
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md5:3c51ff97af9bed959ac17d2b8bd3ca8e
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25 Bytes | Download |
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md5:0f52be74fd4fc1155c5496836c4f95be
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13.1 kB | Download |
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md5:5323a8a619dc2b6a2a5f76465e5c8cf9
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94.4 MB | Download |
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md5:070b8b69ca19ade935c36062faed648d
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3.6 GB | Download |
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md5:4af17d726d7df61ebfa3d92255fe7f70
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84 Bytes | Download |
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md5:19a06e6de0a04e127e069b4c2482253c
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17.1 kB | Download |
Additional details
Related works
- Is referenced by
- Preprint: 10.1101/2020.09.07.285924 (DOI)