Translate a search query between Ovid MEDLINE and PubMed syntax
How MEDLINE Transpose works
First, Transpose looks for all of the boolean operators in your strategy. It assumes that all of the text which are not boolean operators are search terms, and makes a list of all of these.
Transpose then looks at each item in the list in turn. It uses simple pattern matching to identify standard search syntax, and uses these to decide what type of term it is. For instance, if it sees exp something/, it decides that this is a MeSH term.
Once Transpose has decided what type of term it is looking at, it sends the term to be processed accordingly. If you specified Ovid to PubMed, it will take the term and convert it to PubMed syntax, or vice versa if you specified PubMed to Ovid. The process used is similar to Find and Replace.
Some terms require additional processing. For instance, if your term is a MeSH term, Transpose will check to see if it has any subheadings and send the subheading for additional processing before it finishes the conversion. Also, Transpose checks for specific situations in which a warning might be needed, for instance if an exact translation is not available.
We decided to make the conversion as accurate as possible. Thus, if there is not an exact match between the two databases, we have chosen the translation which will provide the search which is as close as possible to the original strategy. In some cases, this may result in a longer strategy than expected.
After Transpose has translated each item in the list, it puts the boolean operators back in between each of the items, and displays the new strategy on the website. It also displays any warnings or suggestions which were relevant.
What MEDLINE Transpose doesn't do
Transpose only looks at the syntax of the search, not the MeSH terms and keywords which you used. If you enter something which is not a MeSH term using MeSH syntax, the programme will translate it as if it were a real MeSH term. That is, if you enter exp Deliberately Silly Example/, Transpose will return "Deliberately Silly Example"[Mesh]. This includes former MeSH terms which have been changed or deleted - Transpose will translate them just as if they were still valid. Likewise, Transpose will not evaluate the quality of your search strategy.
Transpose is only intended for translating between these two versions of MEDLINE. It is not intended for translating to any other Ovid databases, e.g. EMBASE. That being said, if you enter a keyword-only search, and the PubMed tags which you use happen to correspond to search fields in the other Ovid database, it is possible that you could get a usable search strategy. However, if you attempt this, please check over the search strategy carefully, and be aware that it is quite likely that there will be incorrect translations, since you are using Transpose in a way that it was not intended to be used.
The PubMed interface will accept a keyword or phrase without any syntax or tags, and usually will make an attempt to map it to MeSH headings, and otherwise process the request. Transpose does not have the capability to replicate what PubMed does, and simply translates this as an "all fields" search in Ovid MEDLINE, which is PubMed's default output if it can't map the keyword/phrase. If you wish to replicate PubMed's exact translation of a term without syntax, enter your term into PubMed. Look on the right-hand side of your search results for the Search Details box. Then, copy and paste the contents of the Search Details box into Transpose.
Currently Transpose doesn't translate any strategies which involve dates. That is next on our to-do list (as soon as we fix all of the bugsā¦)
Currently Transpose doesn't translate PubMed Filters nor Ovid limits. So, you can enter something like english[lang] OR english.lg., but not Filters: english or "limit search x to english language". We plan to make those available in future (just as soon as we figure out how!)
Table of Ovid Field Codes and PubMed Tags
Warning! Trying to understand Ovid Field Codes and PubMed Tags, especially which ones correspond, may induce nightmares. We're not joking! Ye be warned.
Certain field codes do not currently have an index. As such, we were unable to perform any analysis, we were not able to obtain any examples. We will attempt further analysis at a later date, but for now, will focus on the field code / tag combinations for which there is a known conversion.
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
MeSH Term | exp Mesh Term/ | "Mesh Term"[Mesh] | PubMed autoexplodes | Yes |
Unexploded MeSH Term | Mesh Term/ | "Mesh Term"[Mesh:NoExp] | Yes | |
Focussed MeSH Term | exp *Mesh Term/ | "Mesh Term"[Majr] | Works with and without explode - have shown with explode here | Yes |
MeSH Term with subheading | exp Mesh Term/dt | "Mesh Term/drug therapy"[Mesh] | PubMed automatically explodes subheadings, Ovid does not. In an Ovid-to-PubMed conversion, Transpose provides a warning - in a PubMed-to-Ovid conversion, it includes all exploded subheadings. | Yes |
MeSH Heading, Exploded | .xm. | [mh] | Yes | |
MeSH Heading, Unexploded | .sh. | [mh:noexp] | Yes | |
MeSH Heading Word | .hw. | N/A | Yes - a warning is given. | |
Name of Substance Word | .nm. | [nm] or [supplementary concept] | Yes | |
Pharmacological Action | n/a | [pa] or [pharmacological action] | Closest equivalent is Ovid is to search as if it were a MeSH term | Yes |
Protocol Supplementary Concept | .ps. | [supplementary concept] | Yes | |
Protocol Supplementary Concept Word | .px. | This will work for a supplementary concept which is only one word long, but not for part of a phrase. | Yes - a warning is given. | |
Rare Disease Supplementary Concept | .rs. | [supplementary concept] | Yes | |
Rare Disease Supplementary Concept Word | .rx. | This will work for a supplementary concept which is only one word long, but not for part of a phrase. | Yes | |
Subheading, Exploded | .xs. | [sh] or [subheading] | Ovid version will only accept 2-letter code | Yes |
Subheading, Floating | .fs. | [sh:noexp] or [subheading:noexp] | Yes. |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Abstract | .ab. | N/A | No equivalent in PubMed - closest equivalent is [tiab] | Yes - a warning is given |
All fields | .af. | [All Fields] or [All] | Yes | |
Keyword Heading / Other Term | .kw. | [ot] | Yes | |
Keyword Heading Word | .kf. | N/A | Yes | |
Other abstract | .oa. | This is one of the many fields searched by the [tiab] and [tw] searches in PubMed, but it cannot be searched separately. | ||
Personal Name as Subject | .pn. | [ps] or [subject - personal name] | Yes | |
Text Word (Ovid) | .tw. | Searches in the title and abstract fields in Ovid. Is equivalent to .ti,ab. | Yes | |
Text Words (PubMed) | .ti,ab,oa,sh,fs,pt,rn,pn. | [tw] | Includes all words and numbers in the title, abstract, other abstract, MeSH terms, MeSH subheadings, Publication Types, Substance Names, Personal Name as Subject, Corporate Author, Secondary Source, Comment/Correction Notes, and Other Terms (see Other Term [OT] above) typically non-MeSH subject terms (keywords), including NASA Space Flight Mission, assigned by an organization other than NLM. | Yes |
Title | .ti. | [ti] or [title] | PubMed [ti] additionally searches for collection title. | Yes |
Title/Abstract | .ti,ab,cl,oa,kw. | [tiab] or [title/abstract] | Words and numbers included in a citation's title, collection title, abstract, other abstract, and keywords | Yes |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Affiliation/Institution | .in. | [ad] | Yes | |
EC/RN Number | .rn. | [rn] or [ec/rn number] | Yes | |
Original/Transliterated Title | .ot. | [tt] | Yes |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Author | .au. | [au] or [author] | Ovid requires format: last name, space, first initial, optional truncation, e.g. smith a$. Ovid field .ax. accepts a last name without a first initial. | Yes |
Author, Corporate | .fa. | [cn] or [author - corporate] | For best results, search it in .fa. You can also search the first word of the corporate author in .au. if you truncate, e.g. cochrane*.au. | Yes |
Author, First | .pa. | [1au] or [author - first] | Yes | |
Author Full Name | .fa. | [fau] or [author - full] | Yes | |
Author, Last | n/a | [lastau] or [author - last] | ||
Author Last Name | .ax. | [au] or [author] accepts a last name without a first initial. | Yes | |
Issue/Part | .ip. | [ip] or [issue] | Yes | |
Journal | .jn. | [journal] | Phrase indexed - must have correct version of journal name. | Yes |
Page/Pagination | .pg. | [pg] or [pagination] | Yes | |
PMID/Unique Identifier | .ui. | [pmid] or [uid] | Yes | |
Source | .so. | This is broken up into several tags in PubMed. Investigation of format required before implementation. | ||
Volume | .vo. | [vi] | Yes | |
Year of Publication | .yr. | This can be searched as the first 4 digits if the [dp] field in PubMed. | Yes |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Country/Place of Publication | .cp. | [pl] | Yes | |
ISSN Electronic | .es. | [ta] or [journal] | Yes | |
ISSN Linking | .il. | [ta] or [journal] | Yes | |
ISSN Print | .is. | [ta] or [journal] | Yes | |
Journal ISO/Title Abbreviation | .io. | [ta] | Yes | |
Journal Subset | .sb. | [sb] | Yes | |
Journal Word | .jw. | n/a | Yes - a warning is given. | |
NLM Journal Code | .jc. | [jid] | Yes | |
NLM Journal Name | .nj. | [journal] | .nj. contains the full name of the journal - equivalent to [journal]? Must try more examples. | |
NLM Journal Word | .nw. | n/a | Yes - a warning is given. |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Date, Beginning | .bd. | N/A | No definition nor index provided in Ovid. | |
Date, Completion/Entry | .ed. | [dcom] or [Date - Completion] | In Ovid, format = YYYYMMDD, truncate with * if needed. In PubMed, format = YYYY/MM/DD, truncation is assumed (no symbol needed). | Yes |
Date, Contribution | .cb. | N/A | No definition nor index provided in Ovid. | |
Date, Create | .ez. | [crdt] OR [Date - Create] | In Ovid, format = YYYY MM DD*, mandatory truncation with *. In PubMed, format = YYYY/MM/DD, truncation is assumed (no symbol needed).The Ovid field called Create Date appears to correspond to the value of Entrez Date in PubMed - have contacted Ovid for clarification. | Yes |
Date, Ending | .et. | N/A | No definition nor index provided in Ovid. | |
Date, Entrez | .dt. | [edat] or | In Ovid, format = YYYY MM DD, mandatory truncation with *. In PubMed, format = YYYY/MM/DD, truncation is assumed (no symbol needed). The Ovid field called Entrez Date appears to correspond to the value of Create Date in PubMed - have contacted Ovid for clarification. | Yes |
Date, Mesh | .da. | [mhda] or [Date - Mesh] | In Ovid, format = YYYY MM DD, truncate with * if needed. In PubMed, format = YYYY/MM/DD, truncation is assumed (no symbol needed). | Yes |
Date, Modification/Revision | .rd. | [lr] OR [Date - Modification] | In Ovid, format = YYYYMMDD, truncate with * if needed. In PubMed, format = YYYY/MM/DD, truncation is assumed (no symbol needed). | Yes |
Date of Publication | .dp. | [dp] OR [pdat] OR [DAte - Publication] | In Ovid, format = YYYY MM DD, truncate with * if needed. In PubMed, format = YYYY/MM/DD, truncation is assumed (no symbol needed). In addition to regular date format, pubmed allows the following format: “last X days”[dp]; “last X months”[dp]; “last X year”[dp] and also records date exactly as published in some cases (e.g. winter 2007). | Yes |
Date of Publication, Electronic | .ep. | [dep] | Yes | |
Date, Update | .up. | N/A | ||
Date, Version | .vd. | N/A | ||
Filter | .sb. | [sb] or [filter] | This may sometimes correspond to .sb. in Ovid. Further investigation required before implementation. | .sb. and [sb] are working - more investigation required for [filter] |
Language | .lg. | [la] or [lang] | Yes | |
Publication Type, Exploded | exp Publication Type/ | [pt] or [ptyp] or [publication type] | E.g. exp Review/ | Yes |
Publication Type, Unexploded | .pt. | [pt:noexp] or [ptyp:noexp] or [publication type:noexp] | Yes | |
Status | .st. | [sb] | .st. is one of the searches corresponding to [sb]. | Yes |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Article Identifier | .id. | [aid] | In Ovid, replace any punctuation with spaces. | Yes |
Author Name ID | .ai. | [auid] | Yes | |
DOI/Location ID/Publisher Item Identifier | .do,di. | [lid] | In Ovid, replace any punctuation with spaces. | Yes |
Grant Information | .gr,gc,gi,no,go. | [gr] or [grant number] | Yes | |
Object ID | .oj. | N/A; | No definition nor index provided in Ovid. | |
Other ID | .oi. | There is a field for this in PubMed, but it is not searchable as a tag. Field = OID | ||
PMC Identifier | .pm. | You can search these without tags in PubMed, they're unique enough to just appear. There is a field for this as well, but it is not searchable as a tag. Field = PMC. |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Citation String | .cs. | N/A | No definition nor index provided in Ovid. | |
Comments | .cm. | There are two fields for this in PubMed, but they are not searchable as tags. Fields = CON, CIN | ||
Conflict of Interest | .ci. | [coi] or [cois] | Yes | |
Copyright Index | .cr. | No equivalent identifiable in PubMed. | ||
Gene Symbol | .gs. | N/A | There is a field for this in PubMed, but it is not searchable as a tag. Field = GS. Data was only entered into this field between 1991 and 1995. | |
Gene Symbol Word | .gw. | N/A | There is a field for this in PubMed, but it is not searchable as a tag. Field = GS. Data was only entered into this field between 1991 and 1995. | |
Indexing Method | .ig. | N/A; | No definition nor index provided in Ovid. | |
Investigator | .ir. | [ir] or [investigator] | Yes | |
Investigator Affiliation | .ia. | There is a field for this in PubMed, but it is not searchable as a tag. Field = IRAD. | ||
Investigator Full Name | [fir] | No exact equivalent in Ovid, but you could chop the end off the given names and then search it in .ir. (Format Surname I). | ||
Investigator Name ID | .ix. | I think this might be a mashup of the [fir] field and another piece of data only available in the XML data in PubMed, which is Idenftifier Source. More investigation required. | ||
Note, General | .nt. | This no longer appears in the list of Ovid Search Fields. Has it been retired? | ||
Publication History Status | .ph. | There is a field for this in PubMed, but it is not searchable as a tag. Field = PHST. | ||
Publication Status | .pp. | There is a field for this in PubMed, but it is not searchable as a tag. Field = PST. | ||
Publisher | .pb. | [pubn] | Yes | |
Publishing Model | .pi. | This no longer appears in the list of Ovid Search Fields. Has it been retired? | ||
Record Owner | .ro. | This is listed under OWN in PubMed's Medline format display but there doesn't seem to be a searchable tag. PubMed provides the following suggestion: "The owner search field includes the acronym that identifies the organization that supplied the citation data. Search using owner + the owner acronym, e.g. ownernasa." | ||
Report Number | .rr. | No index provided in Ovid. | ||
Season | .se. | This is for the month or season in which the article was published. Might be searchable as part of the [dp] field - must experiment. | ||
Secondary Source AN | .sa. | This is equivalent of a "word" search in Ovid - searches for part of the Secondary Source ID. No equivalent - [si] requires full ID number. | ||
Secondary Source ID | .si. | [si] or [secondary source id] | Yes | |
Secondary Source Link | .sl. | N/A | Link possibly related to clinicaltrials.org? | |
Space Flight Mission | .sm. | There is a field for this in PubMed, but it is not searchable as a tag. Field = SFM. | ||
Synonyms | .sy. | N/A | ||
Title Comment | .tc. | This no longer appears in the list of Ovid Search Fields. Has it been retired? | ||
Version ID | .vi. |
Name | Ovid Field Code | PubMed Tag | Notes and explanations | Implemented? |
---|---|---|---|---|
Book Accession | .bk. | N/A; | No definition nor index provided in Ovid. | |
Book Authors | .ba. | Format: smith jc or smith j. No index provided in Ovid. Part of .au. - might be searched in [author]? | ||
Book Authors Full Name | .bf. | No index provided in Ovid. Part of .da. - might be searched in [author -full]? | ||
Book Edition | .bn. | No index provided in Ovid. | ||
Book Editors | .be. | Format: smith jc or smith j. No index provided in Ovid. | ||
Book Part | .pr. | This refers to the chapter of the book being cited. No index provided in Ovid. | ||
Book Title | .bt. | No index provided in Ovid. Part of .so. | ||
Book Volume | .bv. | No index provided in Ovid. Part of .so. | ||
Collection Title | .cl. | No index provided in Ovid. | ||
Editor | .ee. | [ed] or [editor] | No index provided in Ovid. | Yes |
Editor Full Name | .fe. | No index provided in Ovid. | ||
Editor Last Name | .ex. | No index provided in Ovid. Part of ee and fe fields. | ||
Equal Contributor | .ec. | N/A | No definition nor index provided in Ovid. | |
ISBN | .ib. | [is] or [isbn] | Yes | |
Media Type | .mt. | Identifies the physical medium of the book citation. No index provided in Ovid. | ||
Section | .sn. | This is a section of the book (a section that is not a chapter). No index provided in Ovid. | ||
Volume Book Title | .vb. | No index provided in Ovid. Part of .so. |
Name | Ovid Syntax | PubMed Syntax | Notes and explanations | Implemented? |
---|---|---|---|---|
All Citations Search | docz.dz | all[sb] | To find all citations in the database. | Yes |
AIDS Subset | aids hiv journals.sb. or limit [previous search] to AIDS | aids[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Bioethics Subset | bioethicsjournals.sb. or limit [previous search] to bioethics | bioethics[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Cancer Subset | limit [previous search] to cancer | cancer[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Complementary and Alternative Medicine Subset | limit [previous search] to Complementary Medicine | cam[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Dietary Supplements Subset | limit [previous search] to Dietary Supplements | dietsuppl[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
History of Medicine Journals Subset | "history of medicine journals".sb. or limit [previous search] to History of Medicine | history[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. For Ovid field tag version, quotes are necessary because of the "of". | Yes |
Space Life Sciences Subset | "national aeronautics and space administration nasa journals".sb. or limit [previous search] to Space Life Sciences. | space[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. For Ovid field tag version, quotes are necessary because of the "and". | Yes |
Systematic Reviews | limit [previous search] to Systematic Reviews | systematic[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Toxicology Subset | limit [previous search] to Toxicology | tox[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Veterinary Science Subset | limit [previous search] to Veterinary Science | veterinary[sb] | To use the Ovid limit version, substitute the search number of interest instead of [previous search]. | Yes |
Free Full Text Subset | free full text[sb] | No equivalent in Ovid. You might be able to find a few of the same results with limit [previous search] to full text, but that would miss many of the free ones and also include any of your institution's subscriptions, so the results would be quite different. | Yes - a warning is given. | |
Full Text Subset | full text[sb] | This finds any articles where full text is available online, including those that are for purchase. No equivalent in Ovid. | Yes - warning is given. | |
Local Full text Subset | limit [previous search] to full text | [check with your library to see if a filter has been set up] | Check with your library to see if a filter has been set up to limit a PubMed search to only the articles in journals to which the library subscribes. However, please note that the Ovid local full text filter and the PubMed one may return very different results. The Ovid interface appears to have a great deal of difficulty in making their full text filter accurate. | No - this search is too dependent on local variables. |
PubMed Central Subset | pubmed pmc[sb] | No equivalent in Ovid. | Yes - a warning is given. | |
Publisher Subset | publisher[sb] | In theory, Ovid has limit [previous search] to publisher, but this limit returns zero results. | Yes - a warning is given. | |
In Process Articles Subset | in process.st. | inprocess[sb] | Yes | |
Medline (Indexed) Articles Subset | medline.st. | medline[sb] | Yes | |
Old Medline Articles Subset | om.sb. or oldmedline citations.st. | oldmedline[sb] | Yes | |
PubMed Not Medline Articles Subset | "pubmed not medline".st. | pubmednotmedline[sb] | The Ovid version requires quotes because of the "not" | Yes |
In Data Review Articles Subset | in data review.st. | indatareview[sb] | Quotes are not necessary for the Ovid one - I checked! | Yes |
Core Clinical Journals (AIM) Subset | aim.sb. | jsubsetaim[text] | The PubMed version may also be entered without the [text] part. | Yes |
Biotechnology Journals Subset (non-Index Medicus) | b.sb. | jsubsetb[text] | The PubMed version may also be entered without the [text] part. This subset is not currently used. | Yes |
Communication Disorders Journals Subset (non-Index Medicus) | c.sb. or limit [previous search] to communication disorders journals | jsubsetc[text] | The PubMed version may also be entered without the [text] part. This subset is not currently used. | Yes |
Dental Journals Subset (non-Index Medicus) | d.sb. | jsubsetd[text] | The PubMed version may also be entered without the [text] part. | Yes |
Bioethics Subset | e.sb. | jsubsete[text] | The PubMed version may also be entered without the [text] part. Includes records from former Bioethicsline database. | Yes |
Foreign Journals Subset (non-Index Medicus) | f.sb. | jsubsetf[text] | The PubMed version may also be entered without the [text] part. This subset is not currently used, and seemed to only contain one journal anyway. | Yes |
Health Administration Subset (non-Index Medicus) | h.sb. | jsubseth[text] | The PubMed version may also be entered without the [text] part. Includes records from former HealthStar Database. | Yes |
Index Medicus Journals Subset | im.sb. | jsubsetim[text] | The PubMed version may also be entered without the [text] part. | Yes |
Population Information Citations Subset (non-Index Medicus) | j.sb. | jsubsetj[text] | The PubMed version may also be entered without the [text] part. This subset is not currently used. Includes records from former(?) Popline database? | Yes |
Consumer Health Journals Subset (non-Index Medicus) | k.sb. | jsubsetk[text] | The PubMed version may also be entered without the [text] part. | Yes |
Nursing Journals Subset (non-Index Medicus) | n.sb. | jsubsetn[text] | The PubMed version may also be entered without the [text] part. | Yes |
History of Medicine Subset | q.sb. | jsubsetq[text] | The PubMed version may also be entered without the [text] part. Includes records from former Histline database. | Yes |
History of Medicine Subset (non-Index Medicus) | qis.sb. | jsubsetqis[text] | The PubMed version may also be entered without the [text] part. | Yes |
Older History of Medicine Subset | qo.sb. | jsubsetqo[text] | The PubMed version may also be entered without the [text] part. | Yes |
Reproduction Journals Subset (non-Index Medicus) | r.sb. | jsubsetr[text] | The PubMed version may also be entered without the [text] part. | Yes |
National Aeronautics and Space Administration (NASA) Journals Subset | s.sb. | jsubsets[text] | The PubMed version may also be entered without the [text] part. Includes records from former Spaceline database. | Yes |
Health Technology Assessment Journals Subset (non-Index Medicus) | t.sb. | jsubsett[text] | The PubMed version may also be entered without the [text] part. Includes records from former Healthstar database. | Yes |
AIDS/HIV Journals Subset | x.sb. | jsubsetx[text] | The PubMed version may also be entered without the [text] part. Includes records from teh former Aidsline database. | Yes |
Disclaimer
Transpose is a simple javascript application with no artificial intelligence system. It is intended to provide a basic conversion between the syntax of two MEDLINE interfaces for the sake of convenience only. It is possible that a mistake or inaccuracy may occur. We make no guarantees, and are not liable if any translations are inaccurate (but if you find a bug, please let us know!). Please check over the translations carefully before using them. Transpose is not a substitute for the judgement of someone trained in the use of Ovid MEDLINE or PubMed.
An understanding of how Transpose works and its limitations - as well as an understanding of the MEDLINE database - will help you in obtaining an accurate and usable translation.