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Developing Search Methods for Systematic Review

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Presentation at: Developing Search Methods for Systematic Review Workshop; September 19, 2015; Sina Trauma and Surgery Research Centre , Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
Included Topics: developing search protocols for systematic reviews, search strategies, search resources, search levels, search operators, management of search results, search and information management methods.

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Developing Search Methods for Systematic Review

  1. 1. Developing Search Methods for Systematic Review Farhad Shokraneh Medical Information Specialist Cochrane Schizophrenia Group Presentation at: Developing Search Methods for Systematic Review Workshop; September 19, 2015; Sina Trauma and Surgery Research Centre , Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran DOI: 10.13140/RG.2.1.2744.6248 Permanent Link: http://dx.doi.org/10.13140/RG.2.1.2744.6248
  2. 2. Introduce yourself, please! 9/19/2015 Farhad Shokraneh 2
  3. 3. What is this workshop about? • Developing your search protocol • Running your searches • Managing your search results and alerts • Documenting and reporting your search 9/19/2015 Farhad Shokraneh 3
  4. 4. Typology of Reviews • Traditional/Narrative Reviews • Scoping Reviews • Systematic Reviews – A research review! • etc. 9/19/2015 Farhad Shokraneh 4
  5. 5. Steps to develop a search protocol • Verifying your research question [Already?] • Turning your research question into PICO • Breaking each PICO concept into keywords • Providing the list of search resources/methods • Developing search strategy for each database • Peer-review of search strategies • Revising the search protocol and finalizing 9/19/2015 Farhad Shokraneh 5
  6. 6. Turning research question into PICO • Extract main concepts also referred as: – PICO/PECO – PICOS – PICOT – etc. 9/19/2015 Farhad Shokraneh 6
  7. 7. PICO for interventional reviews • P for – Patients [age group, gender, etc.] – Population – Problem – Participants • I for – Intervention – Index Test – Exposure 9/19/2015 Farhad Shokraneh 7
  8. 8. PICO for interventional reviews • C for – Comparison [Intervention/Index Test] – Control Group – Comparator • O for – Outcomes [Including Scales and Measurements] • T for – Time 9/19/2015 Farhad Shokraneh 8
  9. 9. PICO for interventional reviews • S for – Study design [research methodology] • S for – Setting [rural/urban, in/outpatient, hospital, EM, etc.] • Anything missing from PICO? – Anatomy [what part of body] – Geography [certain country?] – etc. • Usually we have at least one P, at least one I, and at least one S [study design] in an interventional review search 9/19/2015 Farhad Shokraneh 9
  10. 10. Practice: What is your PICO? • Create and save a word document and name it properly. This document will be your search methods/report at the end 9/19/2015 Farhad Shokraneh 10
  11. 11. Breaking PICO concepts into words • Famous Example: – Concept: • Cancer – Keywords: • Cancer • Cancers • Cancerous • Neoplasm • Neoplasms • Neoplasma • Neoplasmatic [?] • Neoplastic [?] • Tumor • Tumors • Tumour • Tumours • Cyst [?] • Cysts [?] • Malignancy • Malignancies • Malignant • Metastasis • Metastases • Metastatic • Words end in ‘-oma’ [?] – Carcinoma – Carcinogen [?] – etc. • O_0 9/19/2015 Farhad Shokraneh 11
  12. 12. Breaking PICO concepts into words • Why are so many keywords for one concept? – Synonyms [generic drug name vs. commercial drug name] – Derivatives from same root [cancer and cancerous] – Highly relevant/connected word [metastasis] – Specific/broad terms of concept [cancer vs. carcinoma] – British/American spelling variations [tumor] • Aetiology; behaviour; centre; randomised; etc. – Word in other languages – Have I missed anything, share your experience? Consider all the aforementioned roles! 9/19/2015 Farhad Shokraneh 12
  13. 13. Breaking PICO concepts into words • Methods to collect the keywords – Objective Methods • Use Controlled Vocabulary [MeSH, EMTREE, CINAHL Headings, etc.] • Checking previous systematic reviews • Searching for published search strategies [search filters] – Subjective Methods • Your mind • Reading reviews or doing a literature review • Experts write reviews! Ask experts! • Test search results 9/19/2015 Farhad Shokraneh 13
  14. 14. Breaking PICO concepts into words • Medical Subject Heading (MeSH) could be used for several purposes and two of them are related to this workshop: – Using MeSH for collecting words – Using Mesh for subject searching • Using MeSH for collecting words – Accessing and Searching MeSH – Structure of a MeSH Record – Options in MeSH Search Interface – Using Entry terms and MeSH heading as words 9/19/2015 Farhad Shokraneh 14
  15. 15. Practice: Break your PICO down 1. Your mind 2. Experts 3. MeSH 9/19/2015 Farhad Shokraneh 15
  16. 16. Providing the list of search resources/methods • First things first – This list depends on • Your topic • Your time and money • Human resources • Funder’s/grant’s criteria • International guide that you follow • Accessibility of resources • Minimum requirements for publication/presentation • etc. 9/19/2015 Farhad Shokraneh 16
  17. 17. Providing the list of search resources/methods • First Search Level: Databases – Your research questions is about medicine/health? [Broad Topic] • MEDLINE and/or PubMed [What is the difference?] • EMBASE – Yours research question is interventional? [Study Design] • Cochrane Library [CDSR; DARE; HTA; CENTRAL; CMR; NHS EED] – Yours research question is about nursing or psychology? [Specific/Narrow Topic] • CINAHL • PsycINFO – The disease/intervention’s geographical epidemiology [National/Regional Databases] • Chinese Databases for Chinese Traditional Medicine 9/19/2015 Farhad Shokraneh 17
  18. 18. Providing the list of search resources/methods • Second Search Level – Happens in search step • Grey Literature [Please Refer to Webinar] – ClinicalTrials.Gov – WHO ICTRP – Dissertations databases – Reports and guidelines – Conference abstracts databases – Contacting the authors, researchers, and organizations – Hand-searching of journals and conference – Happens during research • Retrospective Approach – References of Screened Full Texts – References of Previous Systematic Reviews • Prospective Approach – Citations to Screened Full Texts 9/19/2015 Farhad Shokraneh 18
  19. 19. Practice: List your search sources 9/19/2015 Farhad Shokraneh 19
  20. 20. Practice: Registration in sources • Please register in – Ovid SP [for MEDLINE] – NCBI [for PubMed] – Cochrane Library • And note your username and password in a safe place • If you have done it before it is not required again, please use your login info and login in Ovid SP 9/19/2015 Farhad Shokraneh 20
  21. 21. Developing search strategy for each database • How to put all words together and make the database understand what we want? • Formulation of search strings [formula?] – A time travel to high school mathematics – Set theory and Venn diagrams 9/19/2015 Farhad Shokraneh 21
  22. 22. Developing search strategy for each database • Boolean Operators – Use OR • among the words that you have collected for one concept • Put whole string between two parentheses to make a ‘set’ • Example – String 1: (Cancer OR Cancers OR Cancerous OR Tumour OR Tumours OR Tumor OR Tumors OR Metastasis OR Metastases OR Metastatic OR Malignancy OR Malignancies OR Malignant OR Neoplasm OR Neoplasms) – String 2: (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal) 9/19/2015 Farhad Shokraneh 22
  23. 23. Developing search strategy for each database • Boolean Operators – Use AND • To compine PICO concepts back together • Example 1. (Cancer OR Cancers OR Cancerous OR Tumour OR Tumours OR Tumor OR Tumors OR Metastasis OR Metastases OR Metastatic OR Malignancy OR Malignancies OR Malignant OR Neoplasm OR Neoplasms) 2. (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal) 3. 1 AND 2 9/19/2015 Farhad Shokraneh 23
  24. 24. Developing search strategy for each database • Boolean Operators – Use NOT • To exclude a set from your search results • We are not using NOT so often • One of popular uses of NOT is in excluding animal studies – We’ll see soon! 9/19/2015 Farhad Shokraneh 24
  25. 25. Developing search strategy for MEDLINE via Ovid SP • So for now this is my search strategy but: 1. (Cancer OR Cancers OR Cancerous OR Tumour OR Tumours OR Tumor OR Tumors OR Metastasis OR Metastases OR Metastatic OR Malignancy OR Malignancies OR Malignant OR Neoplasm OR Neoplasms) 2. (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal) 3. 1 AND 2 Can I make it shorter? Of course! 9/19/2015 Farhad Shokraneh 25
  26. 26. Developing search strategy for MEDLINE via Ovid SP • Truncation or stemming a root word in Ovid SP – Search the root of the word and put $ at the end to get the rest of root variations – Search spelling variation of one or zero character using wild card putting ? in middle or end of a word: Tumo?r? 1. (Cancer$ OR Tumo?r? OR Metasta$ OR Malignan$ OR Neoplas$) 2. (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal) 3. 1 AND 2 9/19/2015 Farhad Shokraneh 26
  27. 27. Developing search strategy for MEDLINE via Ovid SP • What part [field] of the paper do we search? Title, abstract, text words, authors, journal name, publication year! • For field searching in Ovid for title and abstract use ‘default’ field tags after end parenthesis: .ti,ab. 1. (Cancer$ OR Tumo?r? OR Metasta$ OR Malignan$ OR Neoplas$).ti,ab. 2. (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal).ti,ab. 3. 1 AND 2 9/19/2015 Farhad Shokraneh 27
  28. 28. Developing search strategy for MEDLINE via Ovid SP • Adding MeSH for subject searching – Where is my main concepts as MeSH [if exist]? 1. exp Neoplasms/ OR (Cancer$ OR Tumo?r? OR Metasta$ OR Malignan$ OR Neoplas$).ti,ab. 2. exp Aspirin/ OR (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal).ti,ab. 3. 1 AND 2 9/19/2015 Farhad Shokraneh 28
  29. 29. Developing search strategy for MEDLINE via Ovid SP • If you want to add another [set] for study design [for example RCT], you can use the available search filters for example Cochrane MEDLINE [Ovid] filter for RCTs 9/19/2015 Farhad Shokraneh 29
  30. 30. Developing search strategy for MEDLINE via Ovid SP 4. randomized controlled trial.pt. 5. controlled clinical trial.pt. 6. randomized.ab. 7. placebo.ab. 8. drug therapy.fs. 9. randomly.ab. 10. trial.ab. 11. groups.ab. 12. 4 or 5 or 6 or 7 or 8 or 9 or 10 or 11 13. exp animals/ not humans.sh. 14. 12 not 13 9/19/2015 Farhad Shokraneh 30
  31. 31. Developing search strategy for MEDLINE via Ovid SP To sum up the first strategy for MEDLINE via Ovid: 1. exp Neoplasms/ OR (Cancer$ OR Tumo?r? OR Metasta$ OR Malignan$ OR Neoplas$).ti,ab. 2. exp Aspirin/ OR (Aspirin OR Acetylsalicylic Acid OR Acylpyrin OR Aloxiprimum OR Colfarit OR Dispril OR Easprin OR Ecotrin OR Endosprin OR Magnecyl OR Micristin OR Polopirin OR Polopiryna OR Solprin OR Solupsan OR Zorprin OR Acetysal).ti,ab. 3. (randomized controlled trial or controlled clinical trial or pragmatic clinical trial).pt. or (randomi?ed or randomly or placebo or trial or groups).ab. or drug therapy.fs. not (animals not (humans and animals)).sh. 4. 1 AND 2 AND 3 9/19/2015 Farhad Shokraneh 31
  32. 32. Practice: Let’s finish the first strategy • Let your colleague peer-review your search strategy using PRESS check list • Export the search results in EndNote format and name the exported file properly • Save the search and set the alert 9/19/2015 Farhad Shokraneh 32
  33. 33. Operators to be use carefully • NOT [as explained] • Adjacency: e.g. in Ovid SP: spinal adj2 cord • Exact Phrase: e.g. "Spinal Cord" 9/19/2015 Farhad Shokraneh 33
  34. 34. Differences in search among databases MEDLINE via Ovid SP PubMed Cochrane Library Boolean and, or, not AND, OR, NOT and, or, not Set Making () () () Truncation $ * * Wild Card ? Automatically Happens Adjacency adj, adj1, adj2 NEAR, NEAR/1, NEXT Phrase "" "" "" Field Tags .ti. .ab. .ti,ab. .tw,ot. After end parenthesis [ti] [tiab] [tw] After each word :ti :ti,ab :ti,ab,kw MeSH exp Neoplasms/ Neoplasms[MeSH] MeSH descriptor: [Neoplasms] explode all trees 9/19/2015 Farhad Shokraneh 34
  35. 35. Practice: Adopting your MEDLINE Ovid SP search strategy for PubMed Note: Hear is Cochrane’s search strategy for RCTs in PubMed: Separated strings: 1. randomized controlled trial[pt] 2. controlled clinical trial[pt] 3. randomized[tiab] 4. placebo[tiab] 5. drug therapy[sh] 6. randomly[tiab] 7. trial[tiab] 8. groups[tiab] 9. #1 OR #2 OR #3 OR #4 OR #5 OR #6 OR #7 OR #8 10. animals[mh] NOT humans[mh] 11. #9 NOT #10 9/19/2015 Farhad Shokraneh 35
  36. 36. Practice: Adopting your MEDLINE Ovid SP search strategy for PubMed Note: Hear is Cochrane’s search strategy for RCTs in PubMed: One go string: (randomized controlled trial or controlled clinical trial or pragmatic clinical trial).pt. or (randomi?ed or randomly or placebo or trial or groups).ab. or drug therapy.fs. not (animals not (humans and animals)).sh. 9/19/2015 Farhad Shokraneh 36
  37. 37. Practice: Adopting your MEDLINE Ovid SP search strategy for PubMed • Let your colleague peer-review your search strategy using PRESS check list • Export the search results in EndNote format and name the exported file properly • Save the search and set the alert 9/19/2015 Farhad Shokraneh 37
  38. 38. Practice: Adopting your MEDLINE Ovid SP search strategy for Cochrane Library Note: you don’t need to use RCT filter for Cochrane Library • Let your colleague peer-review your search strategy using PRESS check list • Export the search results in EndNote format and name the exported file properly • Save the search and set the alert 9/19/2015 Farhad Shokraneh 38
  39. 39. Limitations in search and publication bias • When to Use Date/Time Limits – When updating a review if you have forgotten to set alert – When the searched concept [disease or intervention] has been emerged since a certain year – Periodical searching [per 5-10 years] to update a project depending on grant, e.g. Burden of disease – When you are searching to study the time trend of a topic – Commissioner’s advises you to limit the search to a certain year onward – Searching for events-related searches for example war or natural disasters – If you need a stratified sample of publications during time periods [for special needs] • You should provide a good reason for limiting the search time 9/19/2015 Farhad Shokraneh 39
  40. 40. Limitations in search and publication bias • Publication type/status limitation – Only journal papers? – How about Grey literature? • ClinicalTrials.gov and WHO ICTRP • Dissertations • Conference Proceedings • There a good examples of change in conclusion of systematic reviews including unpublished/grey literature (e.g. Oseltamivir (Tamiflu)) 9/19/2015 Farhad Shokraneh 40
  41. 41. Limitations in search and publication bias • Language bias: Only English • Database bias: PubMed [Geographical and Language Bias] • Full Text Bias: Only free or open access papers • Published Literature Bias • Date/Time Limitation Bias • All biases should be noticed and mentioned in the systematic review 9/19/2015 Farhad Shokraneh 41
  42. 42. Practice: Working with EndNote • Tricks to be used – Import/export the records – Modifying import filters – Modifying export filters – Using DOI and PMID for updating records – De-duplicating in a few clicks – Full Text Finder 9/19/2015 Farhad Shokraneh 42
  43. 43. Managing your search results • Create an EndNote Library and name it properly • Import all three exported files one by one using the related import filter and note the number of search results per database and total number of results • De-duplication – Check the default de-duplication fields in EndNote – Use find duplicate to find, check and delete them 9/19/2015 Farhad Shokraneh 43
  44. 44. Managing your search results • De-duplication – What causes de-duplication – What are available methods for de-duplication – Note the number of duplicates – There are methods for de-duplication in search step! • EMBASE let’s you to exclude ‘MEDLINE Journals’ • You can use ‘NOT MEDLINE[sb]’ at the end of your string to exclude MEDLINE records in PubMed search • There is an option in some of Ovid SP databases to remove the duplicated 9/19/2015 Farhad Shokraneh 44
  45. 45. Search Methods are Part of Research Methods: Reproducible? • Now you have: – Search Date – Search strategies per database – Total number of search results and duplicates • Could any other researcher repeat this search using your search report and get the same number of results? 9/19/2015 Farhad Shokraneh 45
  46. 46. Screening via checking title/abstract • Using EndNote for Screening – Change of View – Searching for Screening inside EndNote • Using Highlighted Word Document • Note the number of screened records checking the title and abstract 9/19/2015 Farhad Shokraneh 46
  47. 47. Getting the full texts of screened records • EndNote feature • Contacting the authors • Using available online databases/services • Inter-Library Loan 9/19/2015 Farhad Shokraneh 47
  48. 48. Studification: Putting salami back together • Putting separate reports of one study under one study name – Check PICO of two similar papers/reports – Do not delete any relevant report – Contact the authors to make sure they belong to the same study 9/19/2015 Farhad Shokraneh 48
  49. 49. Non-English literature • Check title and abstract with your inclusion/exclusion criteria • Use Google Translate • Contact the authors of the paper • Contacting the authors who have cited the non-English paper • Finding volunteer/fee-based services to do the translation 9/19/2015 Farhad Shokraneh 49
  50. 50. Categorization of Studies in Review • Included Studies • Excluded Studies • Studies Awaiting Assessment: If you could not get the full text or enough info to decide on inclusion/exclusion; it will be mentioned in the review in this section • On-Going Studies: If the records and/or contacting the researchers shows that the study has not been finished yet, the study will be mentioned in the review in this section 9/19/2015 Farhad Shokraneh 50
  51. 51. Search team (at least one librarian/information specialist) AND (at least one expert in the topic) 9/19/2015 Farhad Shokraneh 51
  52. 52. From Search Protocol to Search Report • Structure of the search report • PRISMA Flow Diagram – Use the Word Template in PRISMA Website – Use Review Manager – Use PRISMA Flow Diagram Generator 9/19/2015 Farhad Shokraneh 52
  53. 53. Register you systematic review • Go ‘Cochrane’! • PROSPERO [Cochrane does it for you] • Publish in Systematic Reviews journal 9/19/2015 Farhad Shokraneh 53
  54. 54. Thanks for Your Attention and Question Me, Please! • Feel free to contact me at – farhadshokraneh [at] gmail.com – farhad.shokraneh [at] nottingham.ac.uk 9/19/2015 Farhad Shokraneh 54

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